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1 | 12890863 | [
{
"id": "40d63e07-2d58-4051-9921-5b8913a82752",
"type": "title",
"text": [
"The effect of transforming growth factor beta1 gene polymorphisms in ankylosing spondylitis."
],
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[
0,
94
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},
{
"id": "96bcfe01-16bd-4c43-bf22-fb3635f02e3a",
"type": "abstract",
"text": [
"OBJECTIVES: To determine whether genetic polymorphisms in or near the transforming growth factor beta1 ( TGFB1 ) locus were associated with susceptibility to or severity of ankylosing spondylitis (AS). METHODS: Five intragenic single-nucleotide polymorphisms (SNP) and three microsatellite markers flanking the TGFB1 locus were genotyped. Seven hundred and sixty-two individuals from 184 multiplex families were genotyped for the microsatellite markers and two of the promoter SNPs. One thousand and two individuals from 212 English and 170 Finnish families with AS were genotyped for all five intragenic SNPs. A structured questionnaire was used to assess the age of symptom onset, disease duration and disease severity scores, including the BASDAI (Bath Ankylosing Spondylitis Disease Activity Index) and BASFI (Bath Ankylosing Spondylitis Functional Index). RESULTS: A weak association was noted between the rare TGFB1 +1632 T allele and AS in the Finnish population (P = 0.04) and in the combined data set (P = 0.03). No association was noted between any other SNPs or SNP haplotype and AS, even among those families with positive non-parametric linkage scores. The TGFB1 +1632 polymorphism was also associated with a younger age of symptom onset (English population, allele 2 associated with age of onset greater by 4.2 yr, P = 0.05; combined data set, allele 2 associated with age of onset greater by 3.2 yr, P = 0.02). A haplotype of coding region SNPs ( TGFB1 +869/+915+1632 alleles 2/1/2) was associated with age of symptom onset in both the English parent-case trios and the combined data set (English data set, haplotype 2/1/2 associated with age of onset greater by 4.9 yr, P = 0.03; combined data set, haplotype 2/1/2 associated with greater age of onset by 4.2 yr, P = 0.006). Weak linkage with AS susceptibility was noted and the peak LOD score was 1.3 at distance 2 cM centromeric to the TGFB1 gene. No other linkage or association was found between quantitative traits and the markers. CONCLUSION: This study suggests that the polymorphisms within the TGFB1 gene play at most a small role in AS and that other genes encoded on chromosome 19 are involved in susceptibility to the disease."
],
"offsets": [
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{
"id": "029fbfd5-d042-48b8-99f9-0f740f4dcb34",
"type": "gene",
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"transforming growth factor beta1"
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15,
47
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{
"id": "0b615d3a-de4c-4e4d-9843-86f455dc0fb3",
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"text": [
"TGFB1"
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202,
207
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{
"id": "ea85c34d-9474-40b2-983e-d0b25c031614",
"type": "gene",
"text": [
"TGFB1"
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202,
207
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{
"id": "5cc331a5-399c-4ce7-aad3-27440f6af7b5",
"type": "gene",
"text": [
"TGFB1"
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202,
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"id": "386f0b86-8664-490b-8dda-22b9ea316b46",
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"TGFB1"
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{
"id": "4bb79446-ca70-43b0-a597-aa676b7f91b9",
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"TGFB1"
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202,
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{
"id": "480f3fb7-6a69-4af2-b0ca-d84812742d4f",
"type": "gene",
"text": [
"TGFB1"
],
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202,
207
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],
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{
"id": "0cf8ea55-2aa5-46b5-98f5-8323965a4c92",
"type": "gene",
"text": [
"TGFB1"
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202,
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},
{
"id": "66836e78-5a4e-47c7-ac55-c9408ace08bc",
"type": "variant",
"text": [
"+1632 T"
],
"offsets": [
[
1024,
1031
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "1632T"
}
]
}
] | [] | [] | [] |
2 | 12915397 | [
{
"id": "3a051039-7372-4c10-aa92-e84f5a512d87",
"type": "title",
"text": [
"Uncoupling protein-2 polymorphisms in type 2 diabetes, obesity, and insulin secretion."
],
"offsets": [
[
0,
89
]
]
},
{
"id": "31219e4a-e9da-4ae0-b9be-18b6cba3dc3b",
"type": "abstract",
"text": [
"The onset of type 2 diabetes (T2DM) is preceded by obesity, insulin resistance, and impaired beta-cell function. Uncoupling protein-2 ( UCP2 ) is a widely expressed inner mitochondrial membrane protein. Common polymorphisms of the UCP2 gene have been implicated in diabetes, in obesity, and with changes in UCP2 mRNA levels. We tested the hypothesis that common UCP2 variants influence T2DM susceptibility in four parallel studies of separate populations. We typed the -866 promoter (G/A) variant, a nonsynonymous ( Ala55Val or A55V ) single-nucleotide polymorphism in exon 4, and a 45-nt insertion in the 3'-untranslated (3'UTR) region. Study populations included a case-control population study, a family-based association study, and a metabolic study of individuals who had been characterized for insulin sensitivity and secretion. To evaluate UCP2 mRNA levels, we examined a fourth population of subjects, who had undergone subcutaneous fat biopsy. All three variants showed a trend to an association with T2DM (P = 0.05 to 0.07) in the population but not the family-based association study. The 3' insertion/deletion (3'UTR I/D) variant was associated with body mass index (BMI, P = 0.035) among nondiabetic family members. Haplotype combinations were significantly associated with BMI (P = 0.028), triglyceride levels (P = 0.026), and fasting insulin (P = 0.029); highest values for the three traits were observed in individuals with the heterozygous combination GVI/AVD. In the metabolic study, all three variants were associated with an index of beta-cell compensation for insulin sensitivity (disposition index), particularly in interaction with family membership (P < 0.000001). Individuals homozygous for the -866 A allele had decreased adipose mRNA levels relative to GG homozygous individuals (P = 0.009), but the 3'UTR I/D variant had no impact on mRNA levels. We confirm modest effects of UCP2 variants on BMI and T2DM and show significant effects on insulin secretion in interaction with family-specific factors. However, the associated allele and the effects on gene expression are opposite to those reported previously."
],
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{
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"insulin"
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{
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"Uncoupling protein-2"
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[
0,
20
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{
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"UCP2"
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"UCP2"
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{
"id": "85b79b59-6d0c-47c0-8613-11f35c62abb4",
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"UCP2"
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{
"id": "c53138ed-e6d8-470d-8528-f09da052acd7",
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"UCP2"
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{
"id": "000d3fb8-ff9d-4a80-8355-499af212176c",
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"insulin"
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{
"id": "60d081b1-026d-41c0-a5a6-56ed4b8f3497",
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"UCP2"
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{
"id": "edec5133-6a45-4349-b0b3-c06c1a3b8f73",
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"insulin"
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{
"id": "5864b2fc-8e6a-4055-a28c-8bdcbb429cfc",
"type": "variant",
"text": [
"Ala55Val"
],
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616,
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],
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{
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"A55V"
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630,
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{
"id": "17b15d3a-c06a-463e-968e-d9f12134202b",
"type": "variant",
"text": [
"-866 A"
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1831,
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{
"db_name": "HGVS-like",
"db_id": "-866A"
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]
}
] | [] | [] | [] |
3 | 14523377 | [
{
"id": "c28127ba-5157-4c5d-a5bc-39df0c3f842e",
"type": "title",
"text": [
"SLC11A1 (formerly NRAMP1 ) and susceptibility to visceral leishmaniasis in The Sudan."
],
"offsets": [
[
0,
87
]
]
},
{
"id": "0c280920-0a13-4ded-b573-e2d86e681fab",
"type": "abstract",
"text": [
"Genetic susceptibility to visceral leishmaniasis (VL) is indicated by differences in incidence and clinical phenotypes between ethnic groups in Sudan. In mice, innate susceptibility to Leishmania donovani, the etiological agent of VL, is controlled by Slc11a1 (formerly Nramp1). We therefore examined polymorphisms at SLC11A1 in 59 multicase families of VL from the high-incidence Masalit tribe in Sudan. Multipoint nonparametric analysis in ALLEGRO shows a significant linkage across SLC11A1 (Zlr scores 2.38-2.55; 0.008< or =P< or =0.012; information content 0.88). The extended transmission disequilibrium test shows biased transmission of alleles at 5' polymorphisms in the promoter (P=0.0145), exon 3 (P=0.0037) and intron 4 (P=0.0049), and haplotypes formed by them (P=0.0089), but not for 3' polymorphisms at exon 15 or the 3'UTR. Stepwise logistic regression analysis using a case/pseudo-control data set derived from the 59 families was consistent with main effects contributed by the intron 4 469+14G/C polymorphism. Although the two alleles for 469+14G/C lie on haplotypes carrying different alleles for the functional promoter GTn polymorphism, the latter did not itself contribute separate main effects. Sequence analysis of 36 individuals failed to identify new putative functional polymorphisms in the coding region, intron 1, intron/exon boundaries, intron 4/exon 4a, or in the 3'UTR. One novel promoter polymorphism ( -86G/A ) was located within a putative nuclear factor kappa B binding site that could be functional. Further work will determine whether additional polymorphisms occur upstream in the promoter, which could be in linkage disequilibrium with the intron 4 polymorphism. These studies contribute to knowledge of the role of SLC11A1 in infectious disease."
],
"offsets": [
[
88,
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]
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{
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}
] | [] | [] | [] |
4 | 14635012 | [
{
"id": "187a9068-b890-46d2-972f-a29b88bb3356",
"type": "title",
"text": [
"Association of TNF-beta polymorphism with disease severity among patients infected with hepatitis C virus."
],
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0,
108
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},
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"text": [
"The pathogenesis of chronic hepatitis C virus (HCV) infection remains unclear. Tumour necrosis factor alpha ( TNF-alpha ) is alleged to contribute in the pathogenesis of chronic HCV infection. Single nucleotide polymorphism in TNF-alpha and -beta genes could influence the outcome of HCV infection. The aim was to study single nucleotide polymorphism in TNF-alpha promoter region and Nco I polymorphisms in the TNF-beta gene in patients with chronic hepatitis C. Fifty-two patients with histologically proven chronic hepatitis, who had raised ALT levels (>1.5 x ULN) and were HCV RNA positive, were studied. Genotyping of -308 promoter variant of TNF-alpha was performed by PCR with primers that incorporated an Nco I restriction site. For PCR typing of the TNF-beta Nco I restriction fragment length polymorphism, sequence specific primers were used. Polymorphism in the TNF-alpha G/G, G/A and A/A allele was not different between HCV patients and healthy controls. TNF-beta A/A allele was significantly more common (P = 0.02) in patients (28.8%) as compared to controls (12.8%), whereas no significant difference was observed for TNF-beta G/A and G/G alleles [corrected]. Nco I TNF-beta A/A was strongly associated with -308 TNF-alpha G/G (RR of HCV persistence = 4.9), indicating possible linkage between TNF-beta A/A and TNF-alpha G/G allele. Patients with severe hepatic fibrosis more frequently had the TNF-beta A/A allele as compared to patients with mild disease (P = 0.04). Immunogenetic factors, such as single nucleotide polymorphisms in TNF-beta (A/A allele), may affect the natural course of HCV infection, in particular, the disease progression. Larger studies including cytokine expression profiles are needed to fully understand the contribution of the polymorphisms described in the pathogenesis of chronic hepatitis C."
],
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{
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],
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16,
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]
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}
]
},
{
"id": "e95074d8-b071-4f87-9188-89a426ed2728",
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"-308 TNF-alpha G/G"
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{
"db_name": "HGVS-like",
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}
]
}
] | [] | [] | [] |
5 | 14645199 | [
{
"id": "2314077a-5608-42eb-9936-f5790f20b951",
"type": "title",
"text": [
"An association between variants in the IGF2 gene and Beckwith-Wiedemann syndrome: interaction between genotype and epigenotype."
],
"offsets": [
[
0,
129
]
]
},
{
"id": "80eb6127-afaa-4361-acc6-d2d308d21d6e",
"type": "abstract",
"text": [
"Beckwith-Wiedemann syndrome (BWS) is a fetal overgrowth disorder involving the deregulation of a number of genes, including IGF2 and CDKN1C , in the imprinted gene cluster on chromosome 11p15.5. In sporadic BWS cases the majority of patients have epimutations in this region. Loss of imprinting of the IGF2 gene is frequently observed in BWS, as is reduced CDKN1C expression related to loss of maternal allele-specific methylation (LOM) of the differentially methylated region KvDMR1 . The causes of epimutations are unknown, although recently an association with assisted reproductive technologies has been described. To date the only genetic mutations described in BWS are in the CDKN1C gene. In order to screen for other genetic predispositions to BWS, the conserved sequences between human and mouse differentially methylated regions (DMRs) of the IGF2 gene were analyzed for variants. Four single nucleotide polymorphisms (SNPs) were found in DMR0 ( T123C , G358A , T382G and A402G ) which occurred in three out of 16 possible haplotypes: TGTA, CATG and CAGA. DNA samples from a cohort of sporadic BWS patients and healthy controls were genotyped for the DMR0 SNPs. There was a significant increase in the frequency of the CAGA haplotype and a significant decrease in the frequency of the CATG haplotype in the patient cohort compared to controls. These associations were still significant in a BWS subgroup with KvDMR1 LOM, suggesting that the G allele at T382G SNP (CAGA haplotype) is associated with LOM at KvDMR1 . This indicates either a genetic predisposition to LOM or interactions between genotype and epigenotype that impinge on the disease phenotype."
],
"offsets": [
[
130,
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]
]
}
] | [
{
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40,
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40,
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}
]
},
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"id": "472be749-fd01-4be8-b27e-fcfe17f39ace",
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615,
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]
},
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615,
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]
},
{
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]
},
{
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],
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],
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]
},
{
"id": "bc4ddf30-6fa8-4c3d-9d28-258ac5cbaa65",
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"T382G"
],
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1115,
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}
]
},
{
"id": "d5fa00aa-4014-46a5-a8ed-cc2721ed942e",
"type": "variant",
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"A402G"
],
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1127,
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],
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}
]
},
{
"id": "f80806e4-ec68-4287-9b58-8a3ef620d554",
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"T382G"
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],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T382G"
}
]
}
] | [] | [] | [] |
6 | 14651519 | [
{
"id": "3cdb32ae-e6fc-455b-bccb-a0186971e3d2",
"type": "title",
"text": [
"Association of Fcgamma receptor IIb polymorphism with susceptibility to systemic lupus erythematosus in Chinese: a common susceptibility gene in the Asian populations."
],
"offsets": [
[
0,
169
]
]
},
{
"id": "e362e571-58c4-4740-b638-8caf2ad1de92",
"type": "abstract",
"text": [
"The association of Fcgamma receptor (FcgammaR) polymorphisms with systemic lupus erythematosus (SLE) has been demonstrated in various populations; however, the results have been inconsistent. We recently identified a single-nucleotide polymorphism encoding a non-synonymous substitution, Ile232Thr ( I232T ), of FCGR2B and its association with SLE in Japanese and in Thais. Multiple functional FcgammaR genes with polymorphisms ( FCGR2A , FCGR2B , FCGR3A , and FCGR3B ) cluster in 1q23, and some of them are in linkage disequilibrium (LD). To differentiate contributions from multiple-linked loci, comparison of different populations may provide useful information. In this study, we analyzed the above four FCGR polymorphisms of the Chinese patients and controls for the association with SLE. FCGR2A - H131R , FCGR2B - I232T , FCGR3A - F176V , and FCGR3B genotypes were determined in 167 Chinese patients with SLE and 129 healthy controls. Association was examined using case-control analysis. Allele frequencies of FCGR2B - 232T and FCGR3A - 176F were significantly increased in SLE [odds ratio (OR) = 1.67 and OR = 1.41, respectively]. Interestingly, while these alleles had a tendency of positive LD in the controls, FCGR2B - 232T was in positive association with FCGR3A - 176V in SLE, suggesting that these two alleles were associated with SLE in an independent manner. Comparison between SLE with and without nephritis indicated significant association of FCGR2B - 232T with nephritis (OR = 2.65). When the present results were combined with our previous data on the Japanese and the Thais using meta-analytic methods, highly significant and independent association was observed for FCGR2B and FCGR3A genotypes. These results strongly suggested that FCGR2B is a common susceptibility factor to SLE in the Asians."
],
"offsets": [
[
170,
2015
]
]
}
] | [
{
"id": "32f10cfe-acad-4ef1-9f84-c95b258c718f",
"type": "gene",
"text": [
"FCGR2B"
],
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484,
490
]
],
"normalized": [
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}
]
},
{
"id": "398029e1-89ea-4d3a-aa05-6e097b784388",
"type": "gene",
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"FCGR2A"
],
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603,
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],
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}
]
},
{
"id": "96d90009-93a0-40fb-ac9f-fda9b766a26b",
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"FCGR2B"
],
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484,
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],
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]
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{
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"FCGR3A"
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623,
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],
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]
},
{
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]
},
{
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],
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]
},
{
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],
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484,
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]
},
{
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623,
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]
},
{
"id": "70b809c9-77cd-49be-899d-e81401373b25",
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637,
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]
},
{
"id": "4c8a7f79-4625-4d0c-b7e2-bf9391610d83",
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"FCGR2B"
],
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484,
490
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],
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]
},
{
"id": "00eb4fda-c820-4c88-b18b-a10c7d5c9b1c",
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],
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623,
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],
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}
]
},
{
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"FCGR2B"
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484,
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],
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]
},
{
"id": "3346a6fa-feff-4972-bb17-e5af822d8715",
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],
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623,
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}
]
},
{
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484,
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],
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]
},
{
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],
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484,
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]
},
{
"id": "a6419224-709b-4fcf-bc2e-31c9315bcfeb",
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623,
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484,
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],
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}
]
},
{
"id": "1e1bc861-d13c-4e5c-bbd8-08c64d3c9b70",
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"Ile232Thr"
],
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459,
468
]
],
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}
]
},
{
"id": "e7c51062-2637-4357-a0e4-cb15f25bc632",
"type": "variant",
"text": [
"I232T"
],
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471,
476
]
],
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]
},
{
"id": "606648d1-c25a-4e7c-ad0f-f3930b45fb7c",
"type": "variant",
"text": [
"H131R"
],
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[
980,
985
]
],
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"db_name": "HGVS-like",
"db_id": "H131R"
}
]
},
{
"id": "4a89ad85-f5d3-4e2b-9981-e23654ddd082",
"type": "variant",
"text": [
"I232T"
],
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471,
476
]
],
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}
]
},
{
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"type": "variant",
"text": [
"F176V"
],
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[
1016,
1021
]
],
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"db_name": "HGVS-like",
"db_id": "F176V"
}
]
},
{
"id": "a0c35107-b2c6-49cc-aa6d-861780a7179b",
"type": "variant",
"text": [
"232T"
],
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[
462,
466
]
],
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{
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}
]
},
{
"id": "504e810e-f52a-45f1-8c76-df98cdbf49e1",
"type": "variant",
"text": [
"176F"
],
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[
1228,
1232
]
],
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{
"db_name": "HGVS-like",
"db_id": "176F"
}
]
},
{
"id": "3c8dc7e9-1369-4076-beeb-2161f3411357",
"type": "variant",
"text": [
"232T"
],
"offsets": [
[
462,
466
]
],
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{
"db_name": "dbSNP",
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}
]
},
{
"id": "dab2317a-5ab3-44c4-80cf-aa0f8f307e97",
"type": "variant",
"text": [
"176V"
],
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[
1017,
1021
]
],
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{
"db_name": "HGVS-like",
"db_id": "176V"
}
]
},
{
"id": "6cf2d546-d473-4728-84a4-2606f6f0347a",
"type": "variant",
"text": [
"232T"
],
"offsets": [
[
462,
466
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1050501"
}
]
}
] | [] | [] | [] |
7 | 14651522 | [
{
"id": "ab030e7f-dd9b-4c5f-b96e-dd62841db9eb",
"type": "title",
"text": [
"Chemokine gene polymorphisms associate with gender in patients with uveitis."
],
"offsets": [
[
0,
76
]
]
},
{
"id": "7f73221f-8077-4845-97e3-24d5c931233a",
"type": "abstract",
"text": [
"Uveitis is an inflammatory condition of ocular tissue characterized by leukocyte infiltration, tissue damage, and decreased visual acuity. Chemokines have been implicated in the pathogenesis of uveitis. Polymorphisms in the genes encoding chemokines have been described as affecting chemokine production or function. We analyzed the frequency of single-nucleotide polymorphisms (SNPs) in genes encoding CCL2 (-2518 and -2076) and CCL5 (-403 and -28) in patients with Behcet's disease (BD), a systemic form of uveitis, and patients with retinal vasculitis (RV), an organ-specific form of disease. We report that there was no association between any SNP and disease. However, when segregated on the basis of gender the CCR5 -403 AA genotype was only found in male patients with BD. Similarly, CCL2 genotypes 1/2 were predominant in males, while genotype 4 was significantly associated with disease in female patients with BD. Differences in disease symptoms and severity between males and females have been described in BD and gender-specific genetic differences in chemokine gene function may be involved."
],
"offsets": [
[
77,
1189
]
]
}
] | [
{
"id": "e8cf7785-9f1f-44c2-ac67-7c28dc272811",
"type": "gene",
"text": [
"CCL2"
],
"offsets": [
[
481,
485
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6347"
}
]
},
{
"id": "d6e889aa-63c1-45f0-92ca-fb47624bb826",
"type": "gene",
"text": [
"CCL5"
],
"offsets": [
[
510,
514
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6352"
}
]
},
{
"id": "d83d92bf-35ea-4625-9bd4-7386e89d50e7",
"type": "gene",
"text": [
"CCL2"
],
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481,
485
]
],
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"db_id": "6347"
}
]
},
{
"id": "66077cbb-d4ba-436f-8ae3-6534b9cff762",
"type": "variant",
"text": [
"-403 AA"
],
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[
804,
811
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-403A"
}
]
}
] | [] | [] | [] |
8 | 14673707 | [
{
"id": "96a2db98-c2e8-477f-885b-4c0167b4d1a1",
"type": "title",
"text": [
"Identification of a novel splice site mutation of CLCN5 gene and characterization of a new alternative 5' UTR end of ClC-5 mRNA in human renal tissue and leukocytes."
],
"offsets": [
[
0,
167
]
]
},
{
"id": "6da56781-9482-4b85-9489-b4ad49010811",
"type": "abstract",
"text": [
"Mutations in the CLCN5 gene have been detected in Dent's disease and its phenotypic variants (X-linked recessive nephrolithiasis, X-linked recessive hypophosphatemic rickets, and idiopathic low-molecular-weight proteinuria of Japanese children). Dent's disease is a tubular disorder characterized by low-molecular-weight proteinuria, and nephrolithiasis associated with nephrocalcinosis and hypercalciuria. ClC-5 is the first chloride channel for which a definitive role in the trafficking and acidification-dependent recycling of apical membrane proteins has been established. In the course of CLCN5 SSCP analysis in patients with hypercalciuric nephrolithiasis, we detected a novel mutation at intron 2 of the CLCN5 gene, a T-to-G substitution, located 17 bp upstream of the AG acceptor site CLCN5 gene, a T-to-G substitution, located 17 bp upstream of the AG acceptor site. To determine the effect of IVS2-17 T>G mutation on the correct splicing of intron 2, we studied ClC-5 transcripts in a patient's peripheral blood leukocytes by means of quantitative comparative RT/PCR, and found a new ClC-5 5' UTR isoform characterized by the untranslated exon 1b and by retention of intron 1b. This new isoform--isoform B1--was not correlated with mutation since it was detected also in control leukocytes and in renal tissues of kidney donors, thus confirming its physiological role. By RACE analysis we determined the putative transcriptional start site which is located at intron 1a, 251 nt upstream of the first nucleotide of the untranslated exon 1b. ORF analysis revealed that intron 1b retention in isoform B1 stabilizes the initiation of translation to the AGT at position 297 of the ClC-5 cDNA coding region."
],
"offsets": [
[
168,
1888
]
]
}
] | [
{
"id": "e14a1beb-2830-493e-8aa5-f5c054549049",
"type": "gene",
"text": [
"CLCN5"
],
"offsets": [
[
51,
56
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1184"
}
]
},
{
"id": "9685d880-6b9b-4a51-ad80-ba14d20d6be7",
"type": "gene",
"text": [
"CLCN5"
],
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[
51,
56
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1184"
}
]
},
{
"id": "2370722e-6a9d-4cdf-8c14-5c558c8b6c9e",
"type": "gene",
"text": [
"CLCN5"
],
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[
51,
56
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1184"
}
]
},
{
"id": "b627f1a3-1b7b-4eb4-a157-e0641438c496",
"type": "variant",
"text": [
"mutation at intron 2 of the CLCN5 gene, a T-to-G substitution, located 17 bp upstream of the AG acceptor site"
],
"offsets": [
[
857,
966
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "7053fb89-0970-472d-af77-4ffda6df62b7",
"type": "variant",
"text": [
"IVS2-17 T>G"
],
"offsets": [
[
1079,
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]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "TIVS2-17G"
}
]
}
] | [] | [] | [] |
9 | 14681301 | [
{
"id": "07a0d4ae-5a6f-4899-9672-43fa38f05bad",
"type": "title",
"text": [
"Association of tumor necrosis factor polymorphisms with asthma and serum total IgE ."
],
"offsets": [
[
0,
85
]
]
},
{
"id": "81e6a7ca-06e1-4c0a-b247-72e845628d7c",
"type": "abstract",
"text": [
"Tumor necrosis factors (TNF; TNFA and TNFB ) are major pro-inflammatory cytokines that are thought to be important in the pathogenesis of asthma. However, the functions of genetic polymorphisms in these cytokines have not been thoroughly examined in the context of asthma pathology. In an effort to discover polymorphism(s) in genes whose variant(s) have been implicated in asthma phenotypes, we examined the genetic effects of TNF ( TNFA and TNFB ) polymorphisms on asthma and total serum IgE level. Seven common single-nucleotide polymorphisms (SNP) in TNF genes were genotyped in a Korean asthma cohort (asthmatics n=550, normal controls n=171). Six common haplotypes could be constructed in the TNF gene cluster due to very strong LD between TNFA and TNFB , located 13 kb apart on chromosome 6p21. One SNP ( TNFA -308G>A) showed a significant association with the risk of asthma (P=0.0004). The frequency of TNFA -308A allele-containing genotype in asthmatics (9.8%) was much lower than that in normal controls (22.9%). The protective effects of this polymorphism on asthma were also evident in separated subgroups by atopic status (P=0.05 in non-atopic subjects and P=0.003 in atopic subjects). The most common haplotype of the TNF gene (TNF-ht1[GGTCCGG]) was associated with total serum IgE (immunoglobulin E) levels in asthma patients, especially in non-atopic patients (P=0.004). Genetic variants of TNF might be involved in development of asthma and total serum IgE level in bronchial asthma patients. The results of this study could be helpful to understand the function of important TNF genes in asthma and IgE production."
],
"offsets": [
[
86,
1736
]
]
}
] | [
{
"id": "05ece9b8-0adf-4710-b358-257cdc3dfc9d",
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"text": [
"TNFA"
],
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116,
120
]
],
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"db_id": "7124"
}
]
},
{
"id": "a74ae90f-cb87-48e0-9326-3ae2bf8376c1",
"type": "gene",
"text": [
"TNFB"
],
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127,
131
]
],
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}
]
},
{
"id": "e1c16c8a-089b-4272-ae44-eebbc8d77e58",
"type": "gene",
"text": [
"TNFA"
],
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[
116,
120
]
],
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"db_id": "7124"
}
]
},
{
"id": "a4afe27c-4eb8-4527-a340-930cf5ade96a",
"type": "gene",
"text": [
"TNFB"
],
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[
127,
131
]
],
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{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "c39497fe-1b56-43b5-9417-51863f761abb",
"type": "gene",
"text": [
"IgE"
],
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[
80,
83
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "0c7dd5dc-40a4-4d37-ab99-94986546c03f",
"type": "gene",
"text": [
"TNFA"
],
"offsets": [
[
116,
120
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "c37eb549-715e-4da2-b17c-37d56315eeeb",
"type": "gene",
"text": [
"TNFB"
],
"offsets": [
[
127,
131
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "8dc74eb3-466b-4f9d-83ab-7cdc62b2d628",
"type": "gene",
"text": [
"TNFA"
],
"offsets": [
[
116,
120
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "692882c3-ae53-4075-bf87-76f7c8d4d750",
"type": "gene",
"text": [
"TNFA"
],
"offsets": [
[
116,
120
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "acdd4537-6ce0-4a85-8ba2-f1088e493996",
"type": "gene",
"text": [
"IgE"
],
"offsets": [
[
80,
83
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "5dfc55ac-1f32-4207-8826-8fe3044aa959",
"type": "gene",
"text": [
"IgE"
],
"offsets": [
[
80,
83
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "0c2ce636-2345-4377-b0e8-a25267d81b0a",
"type": "gene",
"text": [
"IgE"
],
"offsets": [
[
80,
83
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
}
] | [] | [] | [] |
10 | 14685824 | [
{
"id": "fd852a0f-0271-4b09-bbd5-68193cfd245a",
"type": "title",
"text": [
"Association between polymorphism of the dopamine transporter gene and early smoking onset: an interaction risk on nicotine dependence."
],
"offsets": [
[
0,
136
]
]
},
{
"id": "2332937c-dbe1-48d9-857c-e51928add904",
"type": "abstract",
"text": [
"Previous studies suggested that a polymorphism in the dopamine transporter gene (SLC6A3) is associated with nicotine dependence and age of smoking onset, but the conclusion was controversial. To detect the association of a G-->A polymorphism (NCBI dbSNP cluster ID: rs27072 ) in 3'-untranslated region of the SLC6A3 with nicotine dependence and early smoking onset, we recruited 253 sibships including 668 nicotine-dependent siblings from a rural district of China. The sibship disequilibrium tests (SDT) showed that the rs27072-A allele is significantly associated with smoking onset < or =18 years (kappa2=9.78, p=0.003 in severely nicotine-dependent smokers, and kappa2=4.24, p=0.058 in total smokers), but not significantly associated with severe nicotine dependence. Conditional logistic regression showed that the risk of early smoking onset by the rs27072-A allele was almost three times greater in severely nicotine-dependent smokers [Odds ratio (OR)=11.3, 95% confidence interval (CI)=1.5-85.6] than that in total smokers. Linear regression showed that rs27072-A allele also increased the risk of nicotine dependence by early smoking onset compared with homozygous rs27072-G genotype . Although these findings are preliminary and need validation, the results suggest that a polymorphism in the SLC6A3 may play important roles in smoking onset, and there may be an interactive effect between the SLC6A3 and early smoking onset on modulating the susceptibility of nicotine dependence."
],
"offsets": [
[
137,
1638
]
]
}
] | [
{
"id": "b63fdbf6-f807-4d99-8fd9-f5d6918869e2",
"type": "gene",
"text": [
"dopamine transporter gene (SLC6A3)"
],
"offsets": [
[
192,
226
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6531"
}
]
},
{
"id": "714da62b-dcf9-4f77-92f3-912be578dcb3",
"type": "variant",
"text": [
"rs27072"
],
"offsets": [
[
406,
413
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
},
{
"id": "52922527-0540-4c63-92fb-f22b441ec34d",
"type": "variant",
"text": [
"rs27072-A allele"
],
"offsets": [
[
662,
678
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
},
{
"id": "0b24e91a-35bf-42e6-b907-19ea13c40e8d",
"type": "variant",
"text": [
"rs27072-A allele"
],
"offsets": [
[
662,
678
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
},
{
"id": "053541e2-54ca-4c58-98e6-fb7ae40b97e7",
"type": "variant",
"text": [
"rs27072-A allele"
],
"offsets": [
[
662,
678
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
},
{
"id": "453a6505-d1f6-4789-b069-095744e151d3",
"type": "variant",
"text": [
"rs27072-G genotype"
],
"offsets": [
[
1321,
1339
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
}
] | [] | [] | [] |
11 | 14693717 | [
{
"id": "09fd2ddb-dc6e-4d36-a556-29d98df9e758",
"type": "title",
"text": [
"Genetic variation at the adiponectin locus and risk of type 2 diabetes in women."
],
"offsets": [
[
0,
82
]
]
},
{
"id": "2a00d122-8888-46cf-ac9a-fa49e4f10220",
"type": "abstract",
"text": [
"Previous data suggesting that polymorphisms in the adiponectin gene were associated with insulin resistance or type 2 diabetes have been inconsistent. We assessed the relationship between five common haplotype-tagging single nucleotide polymorphisms (SNPs) in the adiponectin gene ( -11365C>G , -4034A>C , -3964A>G , +45T>G , and +276G>T ), haplotypes defined by these SNPs, and the risk of type 2 diabetes by conducting a nested case-control study of 642 incident cases of type 2 diabetes and 995 matching control subjects in the Nurses' Health Study. Overall, we did not observe significant differences in genotype or allele frequencies for the five SNPs between the case and control subjects. After adjustment for diabetes risk factors, the -4034 C/C genotype was associated with a reduced risk of diabetes (odds ratio [OR] compared with the A/A genotype = 0.70, 95% CI 0.50-0.99, P = 0.04). In subgroup analyses, the +276 genotype was significantly associated with diabetes risk only among subjects with peroxisome proliferator-activated receptor-gamma ( PPAR gamma ) variant 12Ala allele (OR comparing +276 T alleles with the G/G genotype = 1.69, 1.04-2.75, P = 0.035) or among obese subjects (1.46, 1.03-2.08, P = 0.03). These data suggest a potential interaction between the adiponectin genotype and PPAR gamma genotype or obesity, but these analyses should be considered exploratory and require further investigation in larger studies."
],
"offsets": [
[
83,
1546
]
]
}
] | [
{
"id": "a419c5ac-86d9-418b-8fe7-c2a57a872977",
"type": "gene",
"text": [
"adiponectin"
],
"offsets": [
[
26,
37
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9370"
}
]
},
{
"id": "c3872780-db39-400b-836e-4554f04e7387",
"type": "gene",
"text": [
"adiponectin"
],
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[
26,
37
]
],
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{
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}
]
},
{
"id": "f37ce786-84f3-4e2b-90ed-5eac3a366e75",
"type": "gene",
"text": [
"peroxisome proliferator-activated receptor-gamma"
],
"offsets": [
[
1102,
1150
]
],
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"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "052eb8c2-8094-472e-a065-58b3b67bba5c",
"type": "gene",
"text": [
"PPAR gamma"
],
"offsets": [
[
1154,
1164
]
],
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{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "360b1d04-4738-4692-9fe8-59a0eb26d28a",
"type": "gene",
"text": [
"adiponectin"
],
"offsets": [
[
26,
37
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9370"
}
]
},
{
"id": "cf7d614f-6f54-4512-b51b-c6d8837b42a7",
"type": "gene",
"text": [
"PPAR gamma"
],
"offsets": [
[
1154,
1164
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "8ef28d03-4847-4ba4-9aea-4378b112aa7b",
"type": "variant",
"text": [
"-11365C>G"
],
"offsets": [
[
370,
379
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-11365G"
}
]
},
{
"id": "2de9b7f0-faef-4cc8-b846-b731923a6376",
"type": "variant",
"text": [
"-4034A>C"
],
"offsets": [
[
383,
391
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-4034C"
}
]
},
{
"id": "4cb5d8b6-86bb-45c7-9292-d43d34d96601",
"type": "variant",
"text": [
"-3964A>G"
],
"offsets": [
[
395,
403
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-3964G"
}
]
},
{
"id": "34ba68af-2c4e-4f2d-8434-87290db897c5",
"type": "variant",
"text": [
"+45T>G"
],
"offsets": [
[
407,
413
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2241766"
}
]
},
{
"id": "f74c53ff-def3-4392-930c-08f59ba583f7",
"type": "variant",
"text": [
"+276G>T"
],
"offsets": [
[
421,
428
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G276T"
}
]
},
{
"id": "6ab29530-d680-493d-b25b-72f7caab6318",
"type": "variant",
"text": [
"-4034 C/C"
],
"offsets": [
[
836,
845
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-4034C"
}
]
},
{
"id": "7c0b06b0-561f-49d5-ab7f-b459662e42ee",
"type": "variant",
"text": [
"12Ala"
],
"offsets": [
[
1176,
1181
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "2866402c-202e-46d1-9798-6aea7f8d5e3f",
"type": "variant",
"text": [
"+276 T"
],
"offsets": [
[
1205,
1211
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "276T"
}
]
}
] | [] | [] | [] |
12 | 14693721 | [
{
"id": "bd2e2374-17f5-4d81-ad41-605a3bf5b40f",
"type": "title",
"text": [
"The common -866 G/A polymorphism in the promoter of uncoupling protein 2 is associated with increased carbohydrate and decreased lipid oxidation in juvenile obesity."
],
"offsets": [
[
0,
169
]
]
},
{
"id": "d5e2cd2e-3206-4f3d-a024-44f9727ab258",
"type": "abstract",
"text": [
"Uncoupling protein (UCP) 2 is a member of the mitochondrial transporter superfamily that uncouples proton entry in the mitochondrial matrix from ATP synthesis. Although its physiological role remains to be established, UCP2 is considered a candidate gene for association with energy metabolism and obesity. A common promoter polymorphism, -866 G/A , has been associated with increased UCP2 gene expression and middle-aged adult obesity. In fact, our analysis of 296 juvenile obese and 568 nonobese control subjects revealed no difference in the prevalence of this polymorphism. Insulin and glucose response to oral glucose was comparable across the -866 genotypes. Metabolic studies in 147 of these juvenile obese subjects showed that homozygosity for the UCP2 promoter variant A was associated with important changes in energy metabolism compared with other genotypes, i.e., a 34% increase of carbohydrate oxidation (94 +/- 10 vs. 70 +/- 3 mg.min(-1).m(-2), P = 0.004) and a 23% decrease of lipid oxidation (26 +/- 3 vs. 34 +/- 1 mg.min(-1).m(-2), P = 0.03). Therefore, the juvenile obese subjects who are homozygous for the A variant have an increased ratio (3.6 +/- 1.2) of calories derived from carbohydrates to those from lipids compared with G/A or G/G obese children (1.4 +/- 0.2, P = 0.003), suggesting a role for UCP2 in the partitioning of metabolic fuels."
],
"offsets": [
[
170,
1546
]
]
}
] | [
{
"id": "be636ffb-0201-498d-8123-cffbb60b33a2",
"type": "gene",
"text": [
"Uncoupling protein (UCP) 2"
],
"offsets": [
[
170,
196
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "1f05c52b-325b-4743-864a-40e8ad8e0b8e",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
391,
395
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "02df7df2-012b-4f31-855a-949b98872c1f",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
391,
395
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "3575e95d-efd7-4e84-bc79-56e7cdc35500",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
391,
395
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "47ca26b2-4a59-48d6-b50d-bef399dd18ab",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
391,
395
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "a6fde834-dca4-4de3-926c-0af029390981",
"type": "variant",
"text": [
"-866 G/A"
],
"offsets": [
[
12,
20
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
}
] | [] | [] | [] |
13 | 14705223 | [
{
"id": "7a73a42d-0089-4440-9a4b-6d088a85e53f",
"type": "title",
"text": [
"Interleukin 1alpha single-nucleotide polymorphism associated with systemic sclerosis."
],
"offsets": [
[
0,
86
]
]
},
{
"id": "03e3cd17-15a1-4d9f-a85e-858dbbcc6392",
"type": "abstract",
"text": [
"OBJECTIVE: In systemic sclerosis (SSc), constitutive expression of the proinflammatory and fibrogenic cytokine interleukin 1alpha ( IL-1alpha ) by dermal fibroblasts from the affected skin has been observed. We investigated the association of a single-nucleotide polymorphism at position -889 in the IL-1alpha gene in patients with SSc. METHODS: Genotyping of IL-1alpha -889 polymorphism was performed in 46 patients with SSc and in 150 healthy controls by polymerase chain reaction with sequence-specific primers. All subjects were unrelated Slovak Caucasians. RESULTS: In SSc patients, carriers of the IL-1alpha-889 T allele were significantly overrepresented in comparison with controls (63.0% vs 42.0%; p = 0.01, OR 2.3, 95% CI 1.2-4.6). The frequency of the IL-1alpha-889 T allele was increased in SSc patients (38.0%) in comparison with controls (25.7%; p = 0.02). CONCLUSION: The IL-1alpha -889 polymorphism, previously shown to predispose to increased IL-1 protein expression, may be involved in susceptibility to SSc."
],
"offsets": [
[
87,
1121
]
]
}
] | [
{
"id": "162ec1ee-2c02-4bcb-b7c8-d74a110ae59d",
"type": "gene",
"text": [
"IL-1alpha"
],
"offsets": [
[
219,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3552"
}
]
},
{
"id": "2c1250fe-8532-490f-b444-90d9af46546f",
"type": "gene",
"text": [
"IL-1alpha"
],
"offsets": [
[
219,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3552"
}
]
},
{
"id": "6e756ab9-c442-4b10-ab8c-4bf22f4783e5",
"type": "gene",
"text": [
"IL-1alpha"
],
"offsets": [
[
219,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3552"
}
]
},
{
"id": "839c3b34-7560-4f93-89d4-1647a389003f",
"type": "gene",
"text": [
"IL-1alpha"
],
"offsets": [
[
219,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3552"
}
]
},
{
"id": "60235c79-0579-4cd1-8c43-b3332cf9aa05",
"type": "variant",
"text": [
"IL-1alpha-889 T allele"
],
"offsets": [
[
695,
717
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "53993899-173c-487e-b2ed-85e1b2c699e1",
"type": "variant",
"text": [
"IL-1alpha-889 T allele"
],
"offsets": [
[
695,
717
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
}
] | [] | [] | [] |
14 | 14709372 | [
{
"id": "05ebaeb2-d7fa-49e1-b792-d68191691237",
"type": "title",
"text": [
"Association of gene polymorphisms with coronary artery disease in individuals with or without nonfamilial hypercholesterolemia."
],
"offsets": [
[
0,
127
]
]
},
{
"id": "150c9e68-dd3e-4020-9da7-4beeac0d2dd6",
"type": "abstract",
"text": [
"A substantial proportion of individuals with coronary artery disease (CAD) has concomitant hypercholesterolemia. A large-scale association study was performed to identify separately genes that confer susceptibility to CAD in the absence or presence of nonfamilial hypercholesterolemia. The study population comprised 5248 unrelated Japanese individuals, including 3085 subjects with CAD (2350 men, 735 women) and 2163 controls (1329 men, 834 women). Among all study subjects, 2541 individuals (1688 men, 853 women) had nonfamilial hypercholesterolemia, and 2707 individuals (1991 men, 716 women) did not have this condition. The genotypes for 33 polymorphisms of 27 candidate genes were determined with a fluorescence- or colorimetry-based allele-specific DNA primer-probe assay system. Multivariate logistic regression analysis with adjustment for age, body mass index, and the prevalence of smoking, hypertension, diabetes mellitus, and hyperuricemia revealed that three polymorphisms [ 994G --> T ( Val279Phe ) in the platelet-activating factor acetylhydrolase gene, 242C --> T ( His72Tyr ) in the NADH/NADPH oxidase p22 phox gene, and 1100C --> T in the apolipoprotein C-III gene] were significantly associated with CAD in men with hypercholesterolemia. Genotyping of these three polymorphisms may prove informative for prediction of the genetic risk for CAD in men with nonfamilial hypercholesterolemia."
],
"offsets": [
[
128,
1545
]
]
}
] | [
{
"id": "2b6452b7-1a03-422a-b95c-ceb37f63ec8c",
"type": "gene",
"text": [
"platelet-activating factor acetylhydrolase"
],
"offsets": [
[
1151,
1193
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7941"
}
]
},
{
"id": "2b6acec9-a49d-4063-9b92-fa004490f800",
"type": "gene",
"text": [
"NADH/NADPH oxidase p22 phox"
],
"offsets": [
[
1235,
1262
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "e2980509-872d-4fcb-81af-b1438900c77f",
"type": "gene",
"text": [
"apolipoprotein C-III"
],
"offsets": [
[
1294,
1314
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "345"
}
]
},
{
"id": "fc6a4fda-ff92-41bb-87d9-7266f13c4a16",
"type": "variant",
"text": [
"994G --> T"
],
"offsets": [
[
1117,
1127
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G994T"
}
]
},
{
"id": "ebd62163-63c7-4f34-a0d5-d3fa2da4a88c",
"type": "variant",
"text": [
"Val279Phe"
],
"offsets": [
[
1131,
1140
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "V279F"
}
]
},
{
"id": "92b2e09a-5565-41df-83b6-313003607f79",
"type": "variant",
"text": [
"242C --> T"
],
"offsets": [
[
1202,
1212
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "4673"
}
]
},
{
"id": "a71ab211-4e47-4a25-bb07-3dfec38ee9ae",
"type": "variant",
"text": [
"His72Tyr"
],
"offsets": [
[
1216,
1224
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "4673"
}
]
}
] | [] | [] | [] |
15 | 14712309 | [
{
"id": "5719c533-8dcb-4f32-aa98-b8e3139997eb",
"type": "title",
"text": [
"Polymorphisms in the interleukin-20 gene: relationships to plaque-type psoriasis."
],
"offsets": [
[
0,
83
]
]
},
{
"id": "89ddb893-cb6a-45dc-8861-ef44755d3bf0",
"type": "abstract",
"text": [
"We analyzed the frequency of single-nucleotide polymorphisms (SNPs) at positions -1053 ( rs 2981572 ), 1380 ( rs 2981573 ), 1462 ( rs 2232360 ), and 3978 ( rs 1518108 ) of the human interleukin-20 ( IL-20 ) gene by tetraprimer ARMS-PCR method. A significant association between patients with psoriasis and the G allele at position -1053 (P<0.05) was established. The pairwise linkage disequilibrium (LD) matrix showed that the nearly complete LD was present within the polymorphisms at positions -1053, 1380, and 1462 of the IL-20 gene. We found that patients with plaque psoriasis had a higher frequency of the HT3 GAA haplotype (P<0.01, OR 2.341, 95% CI: 1.346-4.074) compared to the control group. Likewise, the HT3 GAA haplotype was associated with an increased risk of early-onset psoriasis (P<0.01, OR 2.305, 95% CI: 1.285-4.132), late onset of disease (P<0.01, OR 2.542, 95% CI: 1.266-5.102), familial psoriasis (P<0.02, OR 2.220, 95% CI: 1.249-3.945), and sporadic disease (P<0.01, OR 2.523, 95% CI: 1.390-4.580). Our data indicate that IL-20 gene polymorphisms should have a role in determining susceptibility to plaque-type psoriasis. The possible role of the studied SNPs in the regulation of the expression of IL-20 is unknown yet and needs further studies."
],
"offsets": [
[
84,
1367
]
]
}
] | [
{
"id": "531d9f14-559e-4b62-9356-119cde65b296",
"type": "gene",
"text": [
"interleukin-20"
],
"offsets": [
[
22,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "6cb0718a-4d65-43a1-b369-b0df21cf80df",
"type": "gene",
"text": [
"IL-20"
],
"offsets": [
[
285,
290
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "42d26fbd-4b0b-4a95-b763-0d73367c4934",
"type": "gene",
"text": [
"IL-20"
],
"offsets": [
[
285,
290
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "1ca160ee-6ae5-4696-9a48-92ba204d9122",
"type": "gene",
"text": [
"HT3"
],
"offsets": [
[
703,
706
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "144125"
}
]
},
{
"id": "06c6eb7e-086b-4cf1-b072-09bee108642f",
"type": "gene",
"text": [
"HT3"
],
"offsets": [
[
703,
706
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "144125"
}
]
},
{
"id": "faa39339-3be3-4ba1-9543-d43f6048aa1d",
"type": "gene",
"text": [
"IL-20"
],
"offsets": [
[
285,
290
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "00d3c497-5bcc-48be-b8f7-c098c399be95",
"type": "gene",
"text": [
"IL-20"
],
"offsets": [
[
285,
290
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "2f9bb812-fd3f-42c7-9acb-578e3004e596",
"type": "variant",
"text": [
"rs 2981572"
],
"offsets": [
[
173,
183
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2981572"
}
]
},
{
"id": "5f2dfc08-c798-4458-a77d-c941d8bd56ee",
"type": "variant",
"text": [
"rs 2981573"
],
"offsets": [
[
194,
204
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2981573"
}
]
},
{
"id": "49f413d5-88a9-4350-b2a9-58229af82258",
"type": "variant",
"text": [
"rs 2232360"
],
"offsets": [
[
215,
225
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2232360"
}
]
},
{
"id": "d450daf7-ddda-487b-9ef3-15080c679a96",
"type": "variant",
"text": [
"rs 1518108"
],
"offsets": [
[
240,
250
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1518108"
}
]
},
{
"id": "83a407f4-e8ee-4daf-bfd1-915b56b81a85",
"type": "variant",
"text": [
"G allele at position -1053"
],
"offsets": [
[
397,
423
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2981572"
}
]
}
] | [] | [] | [] |
16 | 14715843 | [
{
"id": "2ed1a920-e155-4415-a398-51997fd31dda",
"type": "title",
"text": [
"Ghrelin receptor gene : identification of several sequence variants in extremely obese children and adolescents, healthy normal-weight and underweight students, and children with short normal stature."
],
"offsets": [
[
0,
200
]
]
},
{
"id": "f770c944-728e-4daf-8861-dd068edaf965",
"type": "abstract",
"text": [
"GH secretagogue receptor (GHSR, ghrelin receptor) is involved in regulation of body weight and GH secretion. We initially analyzed two single-nucleotide polymorphisms of the GHSR in up to 184 extremely obese children and adolescents and up to 184 healthy underweight students. The frequency of the 171T allele of rs495225 was higher in our obese samples (75.0%) than in the underweight individuals (70.2%; nominal P = 0.14). This trend could not be substantiated in an additional association study in 270 obese and 145 underweight and normal weight individuals and in a transmission disequilibrium test based on 387 obesity trios (transmission rate of 171T , 51.8%; nominal P = 0.53). Additionally, the coding region of GHSR was systematically screened, and seven sequence variants were identified in 93 obese, 96 normal weight, and 94 underweight individuals and 43 children with short normal stature (SNS). Five silent single-nucleotide polymorphisms showed similar genotype frequencies in the different weight groups and SNS children (all nominal P > 0.3). Two novel missense variants were detected only in one obese carrier and one SNS child, respectively. In conclusion, we did not obtain conclusive evidence for an involvement of the ghrelin receptor gene in body weight regulation or SNS in our study groups."
],
"offsets": [
[
201,
1526
]
]
}
] | [
{
"id": "28745f89-8c15-41a9-93e0-35f598700452",
"type": "gene",
"text": [
"GH secretagogue receptor (GHSR, ghrelin receptor)"
],
"offsets": [
[
201,
250
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2693"
}
]
},
{
"id": "2ef8b153-26e5-4c3d-8bcc-9eaf9ae02d2b",
"type": "gene",
"text": [
"GHSR"
],
"offsets": [
[
227,
231
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2693"
}
]
},
{
"id": "4f2286f6-8c3d-48c7-874e-244be046c92f",
"type": "gene",
"text": [
"GHSR"
],
"offsets": [
[
227,
231
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2693"
}
]
},
{
"id": "f6e8489f-4484-4e67-818d-9631227b9ea6",
"type": "variant",
"text": [
"171T"
],
"offsets": [
[
503,
507
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "495225"
}
]
},
{
"id": "9b54c655-0b53-4afa-8cc1-304074353dad",
"type": "variant",
"text": [
"rs495225"
],
"offsets": [
[
520,
528
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "495225"
}
]
},
{
"id": "ee7993d1-7321-465d-9414-9817e9685141",
"type": "variant",
"text": [
"171T"
],
"offsets": [
[
503,
507
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "495225"
}
]
}
] | [] | [] | [] |
17 | 14715845 | [
{
"id": "42c05b4c-6e3a-49cc-9c1e-de200d2daed1",
"type": "title",
"text": [
"Cytotoxic T lymphocyte-associated molecule-4 polymorphism and relapse of Graves' hyperthyroidism after antithyroid withdrawal."
],
"offsets": [
[
0,
127
]
]
},
{
"id": "3d218e56-12df-40f8-8d3c-2855ca13d4ff",
"type": "abstract",
"text": [
"We studied the A/G single nucleotide polymorphism (SNP) at position 49 in exon 1 of the cytotoxic T lymphocyte-associated molecule-4 gene in 148 Chinese Graves' disease (GD) patients and 171 controls. Our primary aim was to test for the association of this SNP with the relapse of the hyperthyroidism after antithyroid withdrawal. Our secondary aim was to investigate the relationship between GD patients and controls according to the SNP genotypes. All GD patients were divided into the following three groups according to the time of relapse after drug discontinuation: group 1, early relapse within 9 months; group 2, relapse between 10 and 36 months; and group 3, relapse 3 or more years after discontinuation of treatment. There was a significant difference of genotype frequencies (P < 0.001) and allele frequencies (P < 0.001) among the three groups of patients. The frequency of the G/G genotype decreased from 79% to 64% and 39% in groups 1, 2, and 3, respectively. Compared with controls, a strong association (P < 0.001) of G allele was found for group 1, and moderate significance (P = 0.04) was found for group 2, but no association (P = 0.33) was found for group 3. At the end of treatment, the percentage of patients with persistent TSH-receptor antibody was statistically different (A/A, 9.0%; A/G, 20.8%; G/G, 45.5%; P = 0.004). Using 3 yr as the cutoff point for multivariate logistic regression analysis, we found that the G/G genotype (adjusted odds ratio, 3.1 compared with A/G plus A/A; 95% confidence interval, 1.3-7.1), larger goiter size at the end of treatment, and positive TSH-receptor antibody at the end of treatment were independent risk factors of recurrence. We conclude that the A/G polymorphism of the cytotoxic T lymphocyte-associated molecule-4 gene affects the progress of GD. The G/G genotype is associated with poor outcome."
],
"offsets": [
[
128,
1998
]
]
}
] | [
{
"id": "e4dc7f4f-6db8-4b3e-b2df-5978d447d1a9",
"type": "gene",
"text": [
"cytotoxic T lymphocyte-associated molecule-4"
],
"offsets": [
[
219,
263
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "ba5bbf44-9023-4e76-829b-9cccd8e6fbf1",
"type": "gene",
"text": [
"cytotoxic T lymphocyte-associated molecule-4"
],
"offsets": [
[
219,
263
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "56a3e6c2-93f9-4a4e-ae91-0b7b6d543a7c",
"type": "variant",
"text": [
"A/G single nucleotide polymorphism (SNP) at position 49"
],
"offsets": [
[
144,
199
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "231775"
}
]
}
] | [] | [] | [] |
18 | 14729863 | [
{
"id": "7f8aa479-4638-48cb-b473-c6bdc51aabac",
"type": "title",
"text": [
"APOA5 gene variants, lipoprotein particle distribution, and progression of coronary heart disease: results from the LOCAT study."
],
"offsets": [
[
0,
129
]
]
},
{
"id": "acd21656-6eda-4ca0-8c73-9338f5e1928a",
"type": "abstract",
"text": [
"Animal and human studies support a role for apolipoprotein A-V (apoA-V) in triglyceride (TG) metabolism. We examined the relationship of APOA5 -1131T>C and S19W with lipid subfractions and progression of atherosclerosis in the Lopid Coronary Angiography Trial. Compared with -1131TT men (n = 242), carriers of the -1131C allele (n = 54) had significantly higher total TG (P = 0.03), reflected in significantly increased VLDL mass [higher VLDL-TG, VLDL-cholesterol, VLDL-protein, and surface lipids (all P < 0.05)]. Because apoB levels were unaffected by genotype, this suggests an increase in VLDL size and not number. Compared with 19SS men (n = 268), 19W carriers (n = 44) had higher intermediate density lipoprotein (IDL)-TG, IDL-cholesterol (P = 0.04), and IDL-surface components [free cholesterol (P = 0.005) and phospholipids (P = 0.017)] but not protein content, suggesting an increase in IDL lipid enrichment resulting in an increase in IDL size. 19W carriers also showed a trend toward increased progression of atherogenesis, as measured by change in average diameter of segments (-0.46 +/- 0.011 mm compared with -0.016 +/- 0.006 mm) in 19SS men (P = 0.08). There was no effect of genotype on the response of these parameters to gemfibrozil treatment. These results shed new light on the role of APOA5 variants in TG metabolism and coronary heart disease risk."
],
"offsets": [
[
130,
1524
]
]
}
] | [
{
"id": "a210476d-ced4-4fab-9672-d4b24ced3c2b",
"type": "gene",
"text": [
"apolipoprotein A-V (apoA-V)"
],
"offsets": [
[
175,
202
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "116519"
}
]
},
{
"id": "45f3b05a-3424-42ec-b739-8f3d68fbb921",
"type": "gene",
"text": [
"APOA5"
],
"offsets": [
[
0,
5
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "116519"
}
]
},
{
"id": "17028a9f-6a8c-4216-adbb-5d554fdd911e",
"type": "gene",
"text": [
"apoB"
],
"offsets": [
[
666,
670
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "338"
}
]
},
{
"id": "7f9ecd2e-8a8b-4dfd-83e9-03a578b5b4b6",
"type": "gene",
"text": [
"APOA5"
],
"offsets": [
[
0,
5
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "116519"
}
]
},
{
"id": "737d17c8-4c65-4d02-ade5-ebaf8af5805c",
"type": "variant",
"text": [
"-1131T>C"
],
"offsets": [
[
278,
286
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T-1131C"
}
]
},
{
"id": "76ad8332-6872-48a6-af09-b486e827fd04",
"type": "variant",
"text": [
"S19W"
],
"offsets": [
[
293,
297
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
},
{
"id": "1ec09e72-2972-42ba-bf78-08ac1df18900",
"type": "variant",
"text": [
"-1131TT"
],
"offsets": [
[
414,
421
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T-1131T"
}
]
},
{
"id": "0afb498a-eee1-4996-a8d7-46c0d2a1f9f0",
"type": "variant",
"text": [
"-1131C"
],
"offsets": [
[
455,
461
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-1131C"
}
]
},
{
"id": "5c3af14c-65c9-439b-8b89-efa2854aaee7",
"type": "variant",
"text": [
"19SS"
],
"offsets": [
[
778,
782
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
},
{
"id": "72541488-40be-4c8e-9a45-ed6a19e55a9e",
"type": "variant",
"text": [
"19W"
],
"offsets": [
[
294,
297
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
},
{
"id": "7da432db-a1df-403a-8335-5133216a7b40",
"type": "variant",
"text": [
"19W"
],
"offsets": [
[
294,
297
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
},
{
"id": "fd50f843-142f-425f-bf64-5e8b73386044",
"type": "variant",
"text": [
"19SS"
],
"offsets": [
[
778,
782
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
}
] | [] | [] | [] |
19 | 14730381 | [
{
"id": "8adbde8d-e5b5-4c58-8905-353deb03df8d",
"type": "title",
"text": [
"Association of the Pro12Ala and C1431T 1431T variants of PPARG and their haplotypes with susceptibility to Type 2 diabetes."
],
"offsets": [
[
0,
130
]
]
},
{
"id": "f8374098-8b9c-4502-85fe-b431315678b7",
"type": "abstract",
"text": [
"AIMS/HYPOTHESIS: The Pro12Ala polymorphism of peroxisome proliferator-activated receptor (PPAR)gamma has been consistently associated with Type 2 diabetes. The rare Ala12 variant is estimated to reduce the risk of developing Type 2 diabetes by 20 percent. This variant is in linkage disequilibrium with another common variant, T1431 . Both have opposing associations with body weight. We therefore examined the association of specific haplotypes marked by these two variants with susceptibility to Type 2 diabetes. METHODS: We determined the PPARG genotype of a large Scottish cohort of Type 2 diabetic patients ( n=1997) and compared allele frequencies with a cohort of local children ( n=2444) and a middle-aged, population-based cohort from Scotland ( n=1061). RESULTS: Frequency of the Ala12 allele was slightly lower in the Type 2 diabetic cohort than in the children [odds ratio (OR)=0.91, p=0.1]. In contrast, the Ala12 variant was under-represented in the Type 2 diabetic population when compared with similarly aged non-diabetic adults (OR=0.74, p=0.0006). When the Ala12 variant was on a haplotype not bearing the 1431T variant, it conferred greater protection (OR=0.66, p=0.003). However, when it was present in haplotypes containing the 1431T variant (70% of Ala12 carriers), this protection was absent (OR=0.99, p=0.94). CONCLUSIONS/INTERPRETATION: We replicated the finding that the Ala12 variant of PPARgamma affords protection from Type 2 diabetes, and suggest that this protection is modulated by additional common variation at the PPARG locus."
],
"offsets": [
[
131,
1717
]
]
}
] | [
{
"id": "fd5912c7-23c8-4538-95b0-ebda91d0c5ef",
"type": "gene",
"text": [
"peroxisome proliferator-activated receptor (PPAR)gamma"
],
"offsets": [
[
180,
234
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "9b2a873b-47da-4248-aaca-eac2ffa99659",
"type": "gene",
"text": [
"PPARG"
],
"offsets": [
[
63,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "ae6140a7-b4ba-423c-87d4-6bffedbabc55",
"type": "gene",
"text": [
"PPARG"
],
"offsets": [
[
63,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "4d4e46af-78b1-4d90-a6c2-39358c4c2e1a",
"type": "variant",
"text": [
"Pro12Ala"
],
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[
20,
28
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "91f5b4c5-7ebb-47a9-a91b-d055c66651a5",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "83a65aca-5d4d-4554-8402-26aa72798de2",
"type": "variant",
"text": [
"T1431"
],
"offsets": [
[
465,
470
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3856806"
}
]
},
{
"id": "ba18adb8-58a9-40a7-91a5-dee64414888a",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "08aa0dd9-ca1c-42ad-aaec-d2f8217723c5",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "73847687-d84a-4a59-a21c-6598214a15fb",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "67d1f9ac-b5da-40c5-ad43-3583172c73eb",
"type": "variant",
"text": [
"1431T"
],
"offsets": [
[
36,
41
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3856806"
}
]
},
{
"id": "2620a580-49d6-47df-b12f-23f8ad44dbbb",
"type": "variant",
"text": [
"1431T"
],
"offsets": [
[
36,
41
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3856806"
}
]
},
{
"id": "3f196b22-74df-4194-a7e1-5e515ca473aa",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "557d6b01-3331-4e5e-acdd-47992c069ceb",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
}
] | [] | [] | [] |
20 | 14734460 | [
{
"id": "da27afa4-64c7-4d8f-9c0e-15f48773202f",
"type": "title",
"text": [
"Associations between breast cancer susceptibility gene polymorphisms and clinicopathological features."
],
"offsets": [
[
0,
102
]
]
},
{
"id": "1af3e59e-b4fe-4622-a2f4-648a563a27a2",
"type": "abstract",
"text": [
"PURPOSE: Genetic polymorphisms may affect not only cancer development but also cancer progression, and as a result could influence cancer phenotypes. The aim of this study was to examine the relationship between breast cancer susceptibility gene polymorphisms and clinicopathological features. Experimental Design: We genotyped 664 Korean primary breast cancer patients for 17 single-nucleotide polymorphisms (SNPs) in nine genes, using a high-throughput SNP scoring method. RESULTS: CYP1A1 codon 462 Ile/Val or Val/Val variants and the CYP1B1 codon 432 Leu/Val variant were found more in breast cancer patients </=35 years of age at onset than the common homozygote [odds ratio (OR), 1.6 and 1.7, respectively]. In combination analysis of these two SNPs, the OR was 1.9 when one of them was heterozygous or a rare homozygous form, and increased to 2.3 when both were variants (P = 0.006). Cases with Ile/Val at CYP1A1 codon 462 CYP1A1 codon 462 were 2.6-fold and those with Val/Val were 5.1-fold more likely to have first-degree relatives with breast cancer than those with Ile/Ile (P = 0.002). In the haplotype study of BRCA1 , the 2430C / 2731T / 3667G / 4427C / 4956G homozygote showed less estrogen receptor negativity than the most common diplotype (OR, 0.5; 95% confidence interval, 0.26-0.94). TP53 codon 72 Arg/Pro or Pro/Pro variants were associated with negative axillary lymph node status (OR, 0.7; 95% confidence interval, 0.49-0.94). CONCLUSIONS: These results indicate that polymorphisms of some selected breast cancer susceptibility genes are associated with the clinicopathological phenotypes of breast cancer."
],
"offsets": [
[
103,
1747
]
]
}
] | [
{
"id": "c2a3dc1b-ed5c-48f7-a24c-a9e9acd354d5",
"type": "gene",
"text": [
"CYP1A1"
],
"offsets": [
[
588,
594
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1543"
}
]
},
{
"id": "fd200323-d0b3-46cc-b5ad-8c6cfb9176a1",
"type": "gene",
"text": [
"CYP1B1"
],
"offsets": [
[
645,
651
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1545"
}
]
},
{
"id": "48ccac7d-8d3b-4c03-9652-0ee8f47fef0e",
"type": "gene",
"text": [
"CYP1A1"
],
"offsets": [
[
588,
594
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1543"
}
]
},
{
"id": "761068da-3175-47fb-a3eb-e422f6accb58",
"type": "gene",
"text": [
"BRCA1"
],
"offsets": [
[
1236,
1241
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "672"
}
]
},
{
"id": "87c790be-9268-4346-9984-2f65f7ffa52a",
"type": "gene",
"text": [
"TP53"
],
"offsets": [
[
1419,
1423
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "3b14af26-bef0-4a79-9e27-fea6e985a037",
"type": "variant",
"text": [
"462 Ile/Val"
],
"offsets": [
[
603,
614
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1048943"
}
]
},
{
"id": "6457d11e-48f6-4bbd-a941-3aad744db040",
"type": "variant",
"text": [
"432 Leu/Val "
],
"offsets": [
[
660,
672
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1056836"
}
]
},
{
"id": "b3fc5792-04b8-44a8-92ba-fae3d86cf17a",
"type": "variant",
"text": [
"Ile/Val at CYP1A1 codon 462"
],
"offsets": [
[
1013,
1040
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1048943"
}
]
},
{
"id": "46e62ba5-6d7a-4187-b680-c27af26d67b5",
"type": "variant",
"text": [
"2430C"
],
"offsets": [
[
1249,
1254
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "430C"
}
]
},
{
"id": "38850e3e-39d9-481f-88af-105d4937a67a",
"type": "variant",
"text": [
"2731T"
],
"offsets": [
[
1257,
1262
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "2731T"
}
]
},
{
"id": "ab4a81a2-22fc-44da-a685-835436e8fa90",
"type": "variant",
"text": [
"3667G"
],
"offsets": [
[
1265,
1270
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "3667G"
}
]
},
{
"id": "f0a8e7e5-941d-4690-94e5-44280c364a8f",
"type": "variant",
"text": [
"4427C"
],
"offsets": [
[
1273,
1278
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "4427C"
}
]
},
{
"id": "0ab51732-2e72-40c5-98c4-30f4c7ed46a9",
"type": "variant",
"text": [
"4956G"
],
"offsets": [
[
1281,
1286
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1799967"
}
]
},
{
"id": "cc7ba621-5b71-4160-895f-7b0cc78ab2df",
"type": "variant",
"text": [
"72 Arg/Pro"
],
"offsets": [
[
1432,
1442
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1042522"
}
]
}
] | [] | [] | [] |
21 | 14737097 | [
{
"id": "fff8f195-db1f-480f-b962-fbc895418580",
"type": "title",
"text": [
"Both risk alleles for FcgammaRIIA and FcgammaRIIIA are susceptibility factors for SLE: a unifying hypothesis."
],
"offsets": [
[
0,
113
]
]
},
{
"id": "2ade9b7f-bc6c-48d3-a367-180b9cf7e8a9",
"type": "abstract",
"text": [
"The aim of this study was to analyze in families with SLE for the presence of linkage and the structure and transmission of haplotypes containing alleles for the low-affinity Fcgamma receptors. The Fcgamma receptor polymorphisms FcgammaRIIA - 131R/H , FcgammaRIIIA - 176F/V and FcgammaRIIIB- NA1/2 and a polymorphism in the FcgammaRIIB gene were genotyped with RFLP, allele-specific PCR or pyrosequencing. Individual SNPs and haplotypes were tested for linkage in multicase families and for association using contingency tables, transmission disequilibrium test and affected family-based control groups in Swedish and Mexican single-case families. No linkage or association could be detected using the FcgammaR polymorphisms in the multicase families. However, an association was found for both FcgammaRIIA - 131R and IIIA- 176F alleles in the single-case families, but not for IIIB or IIB. Allelic association to SLE was found for a haplotype that included both risk alleles, but not in haplotypes where only one or the other was present. We propose that FcgammaRIIA - 131R and FcgammaRIIIA - 176F are both risk alleles for SLE transmitted primarily, but not exclusively on a single major haplotype that behaves functionally in a situation similar to that of compound heterozygozity."
],
"offsets": [
[
114,
1409
]
]
}
] | [
{
"id": "d8f2cceb-b181-4358-9edd-21fae69316d5",
"type": "gene",
"text": [
"FcgammaRIIA"
],
"offsets": [
[
23,
34
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2212"
}
]
},
{
"id": "a5cf0a95-5ccb-4d2e-942f-20ffbd0e4401",
"type": "gene",
"text": [
"FcgammaRIIIA"
],
"offsets": [
[
41,
53
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2214"
}
]
},
{
"id": "17d18ed9-170a-42d3-9d0d-ef0ba06b597f",
"type": "gene",
"text": [
"FcgammaRIIA"
],
"offsets": [
[
23,
34
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2212"
}
]
},
{
"id": "8c111e44-c182-44df-a613-4f00559fd82e",
"type": "gene",
"text": [
"FcgammaRIIA"
],
"offsets": [
[
23,
34
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2212"
}
]
},
{
"id": "ac290a6c-bcbf-4fee-80af-614ef93cbeba",
"type": "gene",
"text": [
"FcgammaRIIIA"
],
"offsets": [
[
41,
53
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2214"
}
]
},
{
"id": "9134e287-afb8-4279-9e10-32f8c322494f",
"type": "variant",
"text": [
"131R/H"
],
"offsets": [
[
358,
364
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "R131H"
}
]
},
{
"id": "cabe6fc6-186b-4d9f-984e-9e54ee1e067d",
"type": "variant",
"text": [
"176F/V"
],
"offsets": [
[
383,
389
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "F176V"
}
]
},
{
"id": "16f9b2e8-f634-4f97-bf3e-3e97f699a2c3",
"type": "variant",
"text": [
"NA1/2 "
],
"offsets": [
[
409,
415
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "a7b4148d-60bf-4e47-9cff-b4422c67b99e",
"type": "variant",
"text": [
"131R"
],
"offsets": [
[
358,
362
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "131R"
}
]
},
{
"id": "73efdf72-a666-45e9-81e7-6a464bf2c8ae",
"type": "variant",
"text": [
"176F"
],
"offsets": [
[
383,
387
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "176F"
}
]
},
{
"id": "aa8f66cd-e2a9-47d6-813e-a4c09db3dfbb",
"type": "variant",
"text": [
"131R"
],
"offsets": [
[
358,
362
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "131R"
}
]
},
{
"id": "81060b1a-1270-4fb0-b9ce-7cb0e1f288e5",
"type": "variant",
"text": [
"176F"
],
"offsets": [
[
383,
387
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "176F"
}
]
}
] | [] | [] | [] |
22 | 14739420 | [
{
"id": "05949769-c3d5-4f53-83c5-5affd2db49bb",
"type": "title",
"text": [
"Collagen type I alpha2 ( COL1A2 ) is the susceptible gene for intracranial aneurysms."
],
"offsets": [
[
0,
86
]
]
},
{
"id": "ede4ef5d-451f-4904-8cb7-e97bf4c80b86",
"type": "abstract",
"text": [
"BACKGROUND AND PURPOSE: The collagen alpha2(I) gene ( COL1A2 ) on chromosome 7q22.1, a positional and functional candidate for intracranial aneurysm (IA), was extensively screened for susceptibility in Japanese IA patients. METHODS: Twenty-one single nucleotide polymorphisms (SNPs) of COL1A2 were genotyped in genomic DNA from 260 IA patients (including 115 familial cases) (mean age, 59.9 years) and 293 controls (mean age, 61.6 years). Differences in allelic and genotypic frequencies between the patients and controls were evaluated with the chi(2) test. Circular dichroism spectrometry was monitored with collagen-related peptides that mimic triple-helical models of type I collagen with Ala-459 and Pro-459 to estimate the conformation and stability of alterations. RESULTS: Significant genotypic association in the dominant model was observed between an exonic SNP of COL1A2 and familial IA patients (chi(2)=11.08; df=1; P=0.00087; odds ratio=3.19; 95% CI, 2.22 to 6.50). This SNP induces Ala to Pro substitution at amino acid 459 , located on a triple-helical domain. Circular dichroism spectra showed that the Pro-459 peptide had a higher thermal stability than the Ala-459 peptide. CONCLUSIONS: The variant of COL1A2 could be a genetic risk factor for IA patients with family history."
],
"offsets": [
[
87,
1398
]
]
}
] | [
{
"id": "985c5793-1540-40c5-828b-a2690688f84b",
"type": "gene",
"text": [
"collagen alpha2(I) gene"
],
"offsets": [
[
116,
139
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "2889a694-e0ad-4854-8648-07273ccebfec",
"type": "gene",
"text": [
"COL1A2"
],
"offsets": [
[
26,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "218ba7ce-1237-4fc3-8536-6ca7ca3c200a",
"type": "gene",
"text": [
"COL1A2"
],
"offsets": [
[
26,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "19f669a5-b2be-4803-880f-aece2bf253f5",
"type": "gene",
"text": [
"COL1A2"
],
"offsets": [
[
26,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "0ec5364f-83f3-440a-b165-e77693ef4986",
"type": "gene",
"text": [
"COL1A2"
],
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[
26,
32
]
],
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{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "c1794ba7-a18f-4749-9d82-d02ce196485e",
"type": "variant",
"text": [
"Ala-459"
],
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[
785,
792
]
],
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{
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"db_id": "459A"
}
]
},
{
"id": "262880e7-24d4-4223-9a24-7cf5475442b1",
"type": "variant",
"text": [
"Pro-459"
],
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799,
806
]
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"db_id": "459P"
}
]
},
{
"id": "6885cbba-ee98-4f7a-8bca-99a84f1e78e5",
"type": "variant",
"text": [
"Ala to Pro substitution at amino acid 459"
],
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1094,
1135
]
],
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{
"id": "a39f883c-5127-4e7b-a496-aac55dfe62a7",
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},
{
"id": "6aa82973-f4ab-44f8-bd97-55e7a56c2e5c",
"type": "variant",
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"Ala-459"
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785,
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],
"normalized": [
{
"db_name": "HGVS-like",
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}
]
}
] | [] | [] | [] |
23 | 14742985 | [
{
"id": "5df219a7-e20c-4f53-9ac7-0080841e5a3e",
"type": "title",
"text": [
"Relationship between postrenal transplant osteonecrosis of the femoral head and gene polymorphisms related to the coagulation and fibrinolytic systems in Japanese subjects."
],
"offsets": [
[
0,
172
]
]
},
{
"id": "2e514b49-6702-49d2-9f76-58995483ae75",
"type": "abstract",
"text": [
"BACKGROUND: Nontraumatic osteonecrosis of the femoral head (ONFH) is one of the complications that may occur after renal transplantation. We investigated the relationship between the incidence of ONFH and polymorphisms in the genes for plasminogen activator inhibitor (PAI)-1 , which is one of the major regulatory proteins of the fibrinolytic system, and 5,10-methylenetetrahydrofolate reductase ( MTHFR ), which is associated with the plasma levels of homocysteine in Japanese subjects. METHODS: Thirty-one patients with postrenal transplant ONFH and 106 patients without ONFH were selected. Genotypes of PAI-1 4G/5G and MTHFR C677T were determined by direct sequencing of genomic DNA. In addition, plasma PAI-1 antigen (Ag) levels and plasma total homocysteine (tHcy) levels at the steady state were measured. The relationships between the incidence of ONFH and these genotypes, as well as plasma levels of the gene products, were investigated. RESULTS: Plasma PAI-1 Ag levels were the highest in patients with the 4G/4G genotype, and plasma tHcy levels were the highest in patients with TT genotypes of MTHFR C677T . However, the relationship between the incidence of ONFHH and PAI-1 4G/5G or MTHFR C677T was not observed. The relationship between the incidence of ONFH and plasma levels of PAI-1 Ag or tHcy was not observed. CONCLUSIONS: Genotypes of PAI-1 4G/5G and MTHFR C677T or plasma concentrations of PAI-1 Ag and tHcy had no effect on the incidence of ONFH in Japanese subjects, unlike the results of studies performed in white subjects. The effect of genetic background on the pathologic conditions that developed in patients with postrenal transplant ONFH may differ according to race."
],
"offsets": [
[
173,
1910
]
]
}
] | [
{
"id": "35310ea0-c58c-480e-ba33-498f95d7ecc4",
"type": "gene",
"text": [
"plasminogen activator inhibitor (PAI)-1"
],
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[
410,
449
]
],
"normalized": [
{
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"db_id": "5054"
}
]
},
{
"id": "1e3f0f2d-dbde-40af-9807-51877de75b41",
"type": "gene",
"text": [
"5,10-methylenetetrahydrofolate reductase"
],
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531,
571
]
],
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}
]
},
{
"id": "da1a87c9-40aa-4404-a47f-0a5b9889c657",
"type": "gene",
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"MTHFR"
],
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575,
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]
],
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}
]
},
{
"id": "3fee8bf6-3872-4d4d-a1b3-42b1751bb418",
"type": "gene",
"text": [
"PAI-1"
],
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[
784,
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]
],
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}
]
},
{
"id": "697f6168-3742-4c4f-940d-d01e5b12fd9a",
"type": "gene",
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"MTHFR"
],
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[
575,
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]
],
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"db_id": "4524"
}
]
},
{
"id": "c711c658-67df-4cd3-944d-2edac3eb9d13",
"type": "gene",
"text": [
"PAI-1"
],
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[
784,
789
]
],
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{
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}
]
},
{
"id": "5f18a62a-30cd-47f6-9077-0b7fc6a5954a",
"type": "gene",
"text": [
"PAI-1"
],
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[
784,
789
]
],
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{
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}
]
},
{
"id": "57f88726-de23-47be-badb-9b03757e41ec",
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"MTHFR"
],
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575,
580
]
],
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}
]
},
{
"id": "48da086c-6eb6-4582-921c-8b7f76c761f9",
"type": "gene",
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"PAI-1"
],
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784,
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]
],
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}
]
},
{
"id": "9cb9c464-20be-4fc7-8d86-de7bf6780c51",
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"MTHFR"
],
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575,
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]
],
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]
},
{
"id": "8e1bcb8c-7737-4923-a50e-dbadfcbd30ca",
"type": "gene",
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"PAI-1"
],
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784,
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]
],
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}
]
},
{
"id": "87ec1487-5c88-46a0-ba7e-e5fceda715c6",
"type": "gene",
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"PAI-1"
],
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784,
789
]
],
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}
]
},
{
"id": "ec147ead-1b11-48f4-a8f2-b2479ae3a7fc",
"type": "gene",
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"MTHFR"
],
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[
575,
580
]
],
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{
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}
]
},
{
"id": "316f3231-2388-46f8-877e-5bcc67f06dc8",
"type": "gene",
"text": [
"PAI-1"
],
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[
784,
789
]
],
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{
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"db_id": "5054"
}
]
},
{
"id": "d9f38159-0fe2-438b-8e2c-14e5120596e1",
"type": "variant",
"text": [
"4G/5G"
],
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[
792,
797
]
],
"normalized": [
{
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"db_id": "null"
}
]
},
{
"id": "e3257fa7-361a-4c6c-b016-556ea8349cde",
"type": "variant",
"text": [
"C677T"
],
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[
812,
817
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C677T"
}
]
},
{
"id": "0255381f-0919-4005-ad5b-1d09b60b7368",
"type": "variant",
"text": [
"C677T"
],
"offsets": [
[
812,
817
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C677T"
}
]
},
{
"id": "c45c4142-227a-461c-b484-9e95742bfe22",
"type": "variant",
"text": [
"4G/5G"
],
"offsets": [
[
792,
797
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "875321dd-acd4-4d0e-aa6c-a52e15bca9cf",
"type": "variant",
"text": [
"C677T"
],
"offsets": [
[
812,
817
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C677T"
}
]
},
{
"id": "201aad75-fa1a-4d77-bdd8-1fe24af92112",
"type": "variant",
"text": [
"4G/5G"
],
"offsets": [
[
792,
797
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "38a6b3e6-235f-40a8-b0e4-de212270a5cc",
"type": "variant",
"text": [
"C677T"
],
"offsets": [
[
812,
817
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C677T"
}
]
}
] | [] | [] | [] |
24 | 14747301 | [
{
"id": "0eb288ed-031a-4223-bd62-bcfb75d6df76",
"type": "title",
"text": [
"Uncoupling protein 2 promoter polymorphism -866G/A affects its expression in beta-cells and modulates clinical profiles of Japanese type 2 diabetic patients."
],
"offsets": [
[
0,
160
]
]
},
{
"id": "921ebc61-d950-4c08-bb5e-7d0abaa01a79",
"type": "abstract",
"text": [
"Common uncoupling protein 2 ( UCP2 ) promoter polymorphism -866G/A is reported to be associated with its expression in adipose tissue and the risk of obesity in Caucasians. On the other hand, several studies suggested that UCP2 expression in beta-cells is an important determinant of insulin secretion. In the Japanese population, morbid obesity is very rare, and insulin secretion capacity is relatively low as compared with Caucasians. Because UCP2 would link to insulin secretion and obesity, it might explain this ethnic difference. Here, we report that the UCP2 promoter with the A allele showed higher promoter activity in the INS-1 beta-cell line. The frequency of the A allele is higher in our Japanese study than that in Caucasians. Type 2 diabetic patients with the A allele need insulin therapy earlier and showed higher frequency of insulin treatment. Moreover glucose-induced early insulin secretion is significantly lower in patients with the A allele. However, there was no difference in allele frequency between obese and lean type 2 diabetic patients. In conclusion, UCP2 promoter polymorphism -866G/A does not affect obesity in Japanese type 2 diabetic patients but affects its transcription in beta-cells and modulates glucose-induced insulin secretion and eventually insulin requirement in Japanese type 2 diabetic patients. Higher A allele frequency in the Japanese population might partly explain the ethnic difference of insulin secretion capacity."
],
"offsets": [
[
161,
1662
]
]
}
] | [
{
"id": "1ca3c0f7-9474-4939-9cff-d12ffa747eb4",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
191,
195
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "274c2781-40be-4fdd-8ff2-1cbe0154ec35",
"type": "gene",
"text": [
"UCP2"
],
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[
191,
195
]
],
"normalized": [
{
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}
]
},
{
"id": "e0c4037c-ca5a-41d5-a0b7-3d5d1dcc07de",
"type": "gene",
"text": [
"insulin"
],
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[
450,
457
]
],
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}
]
},
{
"id": "19a42c2a-9eb2-4e39-84dc-095fe5e49b2b",
"type": "gene",
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"insulin"
],
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[
450,
457
]
],
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}
]
},
{
"id": "cef8c0f4-48b7-42b0-ae61-4dee1f48ea04",
"type": "gene",
"text": [
"UCP2"
],
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[
191,
195
]
],
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}
]
},
{
"id": "0c1d4586-24aa-4296-8d33-4cec6de67cd7",
"type": "gene",
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"insulin"
],
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[
450,
457
]
],
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}
]
},
{
"id": "34b0add5-b6a7-4a9d-90d8-6fd165dc495e",
"type": "gene",
"text": [
"UCP2"
],
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[
191,
195
]
],
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}
]
},
{
"id": "3d3230b8-608e-46b1-9bac-5440e891d87f",
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"insulin"
],
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[
450,
457
]
],
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}
]
},
{
"id": "e8bc33de-e7e0-41b2-8486-31e9ea46e7b0",
"type": "gene",
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"insulin"
],
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[
450,
457
]
],
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{
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}
]
},
{
"id": "6b112fee-58a6-4165-8ac8-40838e81e97b",
"type": "gene",
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"insulin"
],
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[
450,
457
]
],
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{
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}
]
},
{
"id": "fcd77405-3120-4333-9b57-4a841f20dae3",
"type": "gene",
"text": [
"UCP2"
],
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[
191,
195
]
],
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"db_id": "7351"
}
]
},
{
"id": "6f4febaf-874a-471c-8480-0b438d58e56e",
"type": "gene",
"text": [
"insulin"
],
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[
450,
457
]
],
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{
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}
]
},
{
"id": "f2fda696-d5b0-45fe-a9b3-0f7bd598beaa",
"type": "gene",
"text": [
"insulin"
],
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[
450,
457
]
],
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{
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}
]
},
{
"id": "10a3050b-1274-4424-b5a0-f65aad234a8d",
"type": "gene",
"text": [
"insulin"
],
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[
450,
457
]
],
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{
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"db_id": "3630"
}
]
},
{
"id": "fd11b891-a9a6-4130-85a0-d59714e1aca4",
"type": "variant",
"text": [
"-866G/A"
],
"offsets": [
[
45,
52
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
},
{
"id": "1bc07e6b-ba5a-4a9f-9d4a-98c04f8e0284",
"type": "variant",
"text": [
"-866G/A"
],
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[
45,
52
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
}
] | [] | [] | [] |
25 | 14749980 | [
{
"id": "78fc68cc-0306-4985-b865-2e1a9f5e39b2",
"type": "title",
"text": [
"Association of TAP2 gene polymorphisms in Chinese patients with rheumatoid arthritis."
],
"offsets": [
[
0,
87
]
]
},
{
"id": "0369aa6c-b8ac-4e92-bde3-0cbbb9b33511",
"type": "abstract",
"text": [
"The aim of this study was to investigate the association between the polymorphism of transporters associated with antigen processing ( TAP1 / TAP2 ) genes and rheumatoid arthritis in Chinese patients. A total of 100 RA patients and 99 healthy control subjects were enrolled. Analyses with polymerase chain reaction (PCR) based restrictions were used to identify the polymorphisms of the TAP1 and TAP2 genes, which were mapped on chromosome 6. There was a significant difference in the distribution of the TAP2 gene codon 565 polymorphism frequency between the RA patients and healthy control subjects ( p<0.001). The odds ratio for the risk of the 'A' allele in RA patients was 1.60 (95% CI: 0.82-2.92). No statistical associations in the distribution of the TAP1 gene polymorphism frequency were found between RA patients and controls. There were some physical links found between TAP1 / TAP2 gene polymorphism loci. However, there was no linkage observed from TAP1 / TAP2 gene polymorphisms and HLA-DRB1*04 between RA patients and healthy controls. We concluded that the TAP2 gene codon 565 'A' allele was associated with RA in Chinese patients in Taiwan. Individuals possessing the 'A' allele had a higher incidence of RA. A lack of association of TAP1 gene polymorphisms between RA patients and healthy individuals was noted. The results of this study provide genetic evidence that TAP2 gene codon 565 polymorphism may play a role in RA."
],
"offsets": [
[
88,
1552
]
]
}
] | [
{
"id": "5b57b373-082e-433a-bab7-9a0fc5782890",
"type": "gene",
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"TAP1"
],
"offsets": [
[
224,
228
]
],
"normalized": [
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}
]
},
{
"id": "1479f5b5-51c0-4c12-bc63-c16c0ca02259",
"type": "gene",
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"TAP2"
],
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[
16,
20
]
],
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{
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}
]
},
{
"id": "72e92a69-a948-4f00-9be4-a9763a693665",
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"TAP1"
],
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224,
228
]
],
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}
]
},
{
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],
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16,
20
]
],
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}
]
},
{
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16,
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],
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}
]
},
{
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],
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224,
228
]
],
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}
]
},
{
"id": "6f6582db-eae8-4620-ae5b-d8c0e72ff5b8",
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"text": [
"TAP1"
],
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224,
228
]
],
"normalized": [
{
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}
]
},
{
"id": "20d4499e-0d77-493a-882d-afdb1c19730d",
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"text": [
"TAP2"
],
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16,
20
]
],
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"db_id": "6891"
}
]
},
{
"id": "b138e724-c5b5-410f-b114-ad20400d0ca4",
"type": "gene",
"text": [
"TAP1"
],
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224,
228
]
],
"normalized": [
{
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}
]
},
{
"id": "4966f8ef-441f-4425-ae2c-7e6a8cb590c4",
"type": "gene",
"text": [
"TAP2"
],
"offsets": [
[
16,
20
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6891"
}
]
},
{
"id": "c494b22d-8241-43db-958a-e193e201b2d4",
"type": "gene",
"text": [
"TAP2"
],
"offsets": [
[
16,
20
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6891"
}
]
},
{
"id": "bf9a77f0-df58-4a60-8c7b-45b8fb8ad87e",
"type": "gene",
"text": [
"TAP1"
],
"offsets": [
[
224,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6890"
}
]
},
{
"id": "e0af70a0-b74e-4ac1-ad29-8193cd66019c",
"type": "gene",
"text": [
"TAP2"
],
"offsets": [
[
16,
20
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6891"
}
]
},
{
"id": "d247fb00-9bb9-4cc5-a674-0fb443beff10",
"type": "variant",
"text": [
"HLA-DRB1*04"
],
"offsets": [
[
1099,
1110
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "a925fd78-6622-43e1-ac98-4af6d616511c",
"type": "variant",
"text": [
"565 'A' "
],
"offsets": [
[
1195,
1203
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2228396"
}
]
}
] | [] | [] | [] |
26 | 14752243 | [
{
"id": "b51de786-9344-4b07-8ad7-4890e41ff115",
"type": "title",
"text": [
"MDR1 haplotypes modify BEN disease risk: a study in Bulgarian patients with Balkan endemic nephropathy compared to healthy controls."
],
"offsets": [
[
0,
133
]
]
},
{
"id": "c38710f9-6aaf-4d45-9a9e-a59a7b40ce55",
"type": "abstract",
"text": [
"BACKGROUND: Balkan endemic nephropathy (BEN) is a slow progressive nephropathy with frequent occurrence of uroepithelial tumors in the upper urinary tract. Genetic factors involved in xenobiotic detoxification mechanisms may cause genetic predisposition to BEN and influence the risk for this disease. Polymorphic MDR1 variants with decreased P-glycoprotein (P-gp) activity modulate the risk for renal neoplasm. We have therefore investigated the impact of MDR1 polymorphisms on BEN manifestation. METHODS: The constitutional genotype frequencies of two SNPs ( C3435T and G2677T ) in the MDR1 gene in 112 healthy control subjects were investigated and compared with those of 96 patients with BEN. Identification of the SNPs was done with rapid cycle real-time PCR and melting curve analysis with allele-specific probes. RESULTS: The frequency of mutant alleles was comparable in both groups. Significant differences were revealed when the MDR1 haplotypes were analyzed. Individuals with a predicted haplotype 12 (2677G/3435T) were less frequent in BEN cases (frequency 7.3%) than in controls (16.1%, p = 0.006). We found that carriers of the haplotype 12 had a decreased risk for BEN (OR = 0.411; 0.21-0.78). CONCLUSIONS: The data suggest that haplotype 12 is protective against BEN. There is no clear molecular explanation of the MDR1 haplotype effects on the protein activity, which can explain the modified effect of the haplotype 12 on BEN risk."
],
"offsets": [
[
134,
1597
]
]
}
] | [
{
"id": "307f4183-7b82-4d3f-920d-6335ed73ecd5",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "b0c1cc2f-bc09-4b0d-b96e-15d9de9ab401",
"type": "gene",
"text": [
"P-glycoprotein (P-gp)"
],
"offsets": [
[
480,
501
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "2cd7b4b4-a756-4d6d-aff1-b4f5e86c462e",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "79833a71-45a3-40a8-9330-c5687cd0df8e",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "47d365e3-8e6e-4b86-94c8-c08c98c3439d",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "94cf8b69-0db0-40b7-8185-5d6ca10fc200",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "b6a2ee46-6ea2-4325-8d0c-b07c26a4fa30",
"type": "variant",
"text": [
"C3435T"
],
"offsets": [
[
701,
707
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1045642"
}
]
},
{
"id": "ba08eb5e-ef68-486a-ba2a-479234857d89",
"type": "variant",
"text": [
"G2677T"
],
"offsets": [
[
714,
720
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2032582"
}
]
}
] | [] | [] | [] |
27 | 14755442 | [
{
"id": "2e350ae6-ed7b-4556-9ec1-1e2d44ad9d88",
"type": "title",
"text": [
"TNXB locus may be a candidate gene predisposing to schizophrenia."
],
"offsets": [
[
0,
66
]
]
},
{
"id": "f4da333a-b734-4850-938f-9abed7db1fc1",
"type": "abstract",
"text": [
"We report here on the detection of nine single nucleotide polymorphisms (SNPs) near to the NOTCH4 locus in the search for schizophrenia susceptibility genes in the class III region of the human major histocompatibility complex (MHC). We totally analyzed 122 family trios recruited in the UK. The TDT analysis demonstrated that of the nine SNPs, three were associated with schizophrenia, including rs1009382 (P = 0.00047), rs204887 (P = 0.007), and rs8283 (P = 0.015). Both rs1009382 and rs204887 are present in the TNXB locus. The rs1009382 is a non-synonymous SNP located in exon 23 of the gene and its A to G base change causes a Glu2578Gly substitution. The goodness-of-fit test showed that genotypic distribution of rs1009382 was deviated from Hardy-Weinberg equilibrium due to homozygote excess in the patient group (P = 0.01), suggesting that a double dose of a genetic risk may be involved. Possibly, rs1009382 is a candidate SNP predisposing to a schizophrenic illness. Moreover, the test for linkage disequilibrium (LD) between paired SNPs showed that the nine SNPs studied may be in the same LD block with an unexpected pattern as the strength of LD was not correlated with the distance between paired SNPs. The haplotype analysis suggested that there might be more than one disease-related allele located in the class III region of the MHC, and that these alleles possibly confer either susceptibility or resistance to schizophrenia."
],
"offsets": [
[
67,
1533
]
]
}
] | [
{
"id": "979e83f7-915a-4b78-9729-8714e25ba13a",
"type": "gene",
"text": [
"NOTCH4"
],
"offsets": [
[
159,
165
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4855"
}
]
},
{
"id": "a6a6e5c7-b0b5-48f4-93bb-f966404764f4",
"type": "gene",
"text": [
"TNXB"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7148"
}
]
},
{
"id": "d5cd3e26-6d2b-4c1e-b6c1-6e9214001dc8",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "da664296-83cb-4f27-9382-d906e3306b72",
"type": "variant",
"text": [
"rs204887"
],
"offsets": [
[
494,
502
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "204887"
}
]
},
{
"id": "1dc454fd-64cb-4d31-9b37-e48ba9aa81ee",
"type": "variant",
"text": [
"rs8283"
],
"offsets": [
[
522,
528
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "8283"
}
]
},
{
"id": "f8f854f2-b07d-49dc-a9fa-a1d2a5d2f1f4",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "b8d30d1e-056f-4895-85c1-2838a82a10aa",
"type": "variant",
"text": [
"rs204887"
],
"offsets": [
[
494,
502
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "204887"
}
]
},
{
"id": "27fbea7e-8718-4633-8645-97a6a4a1472f",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "34adcdb1-b9a4-469e-93c3-961e1cf3f2bc",
"type": "variant",
"text": [
"Glu2578Gly"
],
"offsets": [
[
716,
726
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "fee1e9d0-cf18-43fe-955b-aa83585fbe0a",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "f523305d-a8f9-48cb-af7d-c9b8f4e175fd",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
}
] | [] | [] | [] |
28 | 14755445 | [
{
"id": "dce5b786-ef90-40d9-8943-ac5dc8e2b3f5",
"type": "title",
"text": [
"No association between the APOE gene and autism."
],
"offsets": [
[
0,
50
]
]
},
{
"id": "3c31c46e-3b7f-4c5e-b7f4-0322aa3d53b6",
"type": "abstract",
"text": [
"Autism is a neurodevelopmental disorder characterized by stereotypic and repetitive behavior and interests, together with social and communicative deficiencies. The results of several genomic screens suggest the presence of an autism susceptibility locus on chromosome 19p13.2-q13.4. The apolipoprotein E ( APOE ) gene on chromosome 19 encodes for a protein, apoE , whose different isoforms (E2, E3, E4) influence neuronal growth. APOE participates in lipid transport and metabolism, repair, growth, and maintenance of axons and myelin during neuronal development. The APOE protein competes with the Reelin protein for VLDL/ APOE R2 receptor binding. Several studies have reported evidence for an association between autism and the Reelin gene. Based on these data we tested for association between APOE and autism using family-based association methods in a data set of 322 autism families. Three promoter, one intronic, and one 3' UTR single nucleotide polymorphisms (SNPs) in the APOE gene ( -491a/t , -427c/t , -219g/t , 113c/g , and 5361c/t ) as well as the APOE functional polymorphism (E2, E3, E4) were examined and failed to reveal significant evidence that autism is associated with APOE ."
],
"offsets": [
[
51,
1271
]
]
}
] | [
{
"id": "bf24c118-1fd4-47ed-a216-a3d861a3fbd2",
"type": "gene",
"text": [
"apolipoprotein E "
],
"offsets": [
[
340,
357
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "a37bd779-e7e7-4b49-bad0-8359e8cda2f2",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "82817105-0596-4382-b142-049b9678f837",
"type": "gene",
"text": [
"apoE"
],
"offsets": [
[
413,
417
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "c96bb4ea-8419-4625-b276-a09236e8e1aa",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "3937bc2e-7f95-4f9e-aec6-849f2a2c99d9",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "67c1c034-2cb8-4876-9a92-e9d763337ce3",
"type": "gene",
"text": [
"Reelin"
],
"offsets": [
[
659,
665
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5649"
}
]
},
{
"id": "7add8d05-075b-4acc-af0e-490845fffbfd",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "c21f7363-7509-4f74-804d-2be1cc48eacd",
"type": "gene",
"text": [
"Reelin"
],
"offsets": [
[
659,
665
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5649"
}
]
},
{
"id": "2a6aa8b9-eeff-466d-a982-97fc47288b4a",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "d4ab1259-51ac-4095-a7b9-68647dea129a",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "541b5bdb-dba5-4286-aa96-3d03bcabde98",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "5c077cfd-0cff-4d6b-8cc8-040489dc018a",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "aa7199f9-dae7-4c53-895d-f89b14e6e76f",
"type": "variant",
"text": [
"-491a/t"
],
"offsets": [
[
1061,
1068
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-491T"
}
]
},
{
"id": "e1cae161-5721-4ee0-b842-98def4c8676c",
"type": "variant",
"text": [
"-427c/t"
],
"offsets": [
[
1072,
1079
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-427T"
}
]
},
{
"id": "c0ada70b-2a68-44e4-9c88-999318ae4c5f",
"type": "variant",
"text": [
"-219g/t"
],
"offsets": [
[
1083,
1090
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-219T"
}
]
},
{
"id": "3855b7ca-19f5-4e0d-b868-21346c908d1a",
"type": "variant",
"text": [
"113c/g"
],
"offsets": [
[
1094,
1100
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C113G"
}
]
},
{
"id": "8793094e-2874-49e0-805e-d966510c0ae0",
"type": "variant",
"text": [
"5361c/t"
],
"offsets": [
[
1108,
1115
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C5361T"
}
]
}
] | [] | [] | [] |
29 | 14755451 | [
{
"id": "6e7866bc-4ec0-4536-943c-f7d1a5fe251f",
"type": "title",
"text": [
"No association between the insulin degrading enzyme gene and Alzheimer's disease in a Japanese population."
],
"offsets": [
[
0,
108
]
]
},
{
"id": "2f7da9c6-a9c0-4785-9b90-19c8f84f472b",
"type": "abstract",
"text": [
"Susceptibility to Alzheimer's disease (AD) is thought to be regulated by multiple genetic factors. Recently, three independent studies have reported that loci on chromosome 10q are linked with AD, and the insulin degrading enzyme ( IDE ; MIM 146680) gene located on chromosome 10q23-q25; IDE is located close to the maker D10S583, which exhibits a maximum LOD score for late-onset AD. We examined seven polymorphisms in the IDE gene, the marker D10S583 in the 5' flanking region, and SNPs in introns 1, 3, 11, 20, 21, and 22 ( rs#1999764 , 1855915 , 1970244 , 538469 , 551266 , and 489517 , respectively). Four SNPs in introns 3, 11, 20, and 22 did not exhibit any polymorphisms in the Japanese population that was studied. D10S583 and two SNPs in introns 1 and 21 did not exhibit a significant association with early- or late-onset AD. In addition, no associations were observed for subgroups of AD grouped according to APOE status. The present study indicates that the IDE gene polymorphisms do not confer susceptibility to early- or late-onset AD at least in a Japanese population."
],
"offsets": [
[
109,
1208
]
]
}
] | [
{
"id": "52b0878f-69fc-4e8d-84a0-404a575cd721",
"type": "gene",
"text": [
"insulin degrading enzyme"
],
"offsets": [
[
28,
52
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "1a65d751-af68-41a1-abf6-fa966487c3a3",
"type": "gene",
"text": [
"IDE"
],
"offsets": [
[
343,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "4a0db4f6-8c42-4ac2-bbc6-e92ba5530256",
"type": "gene",
"text": [
"IDE"
],
"offsets": [
[
343,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "6b82ed17-5032-4724-a27d-9bd0e555ad1c",
"type": "gene",
"text": [
"IDE"
],
"offsets": [
[
343,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "2d13d83f-fbab-4228-8e46-a1fa55de2bd0",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
1042,
1046
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "42579967-e581-47bd-a8f7-13bfb554fc38",
"type": "gene",
"text": [
"IDE"
],
"offsets": [
[
343,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "8f7e3345-7c70-4cac-8c08-8d89c5ff4858",
"type": "variant",
"text": [
"rs#1999764"
],
"offsets": [
[
642,
652
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1999764"
}
]
},
{
"id": "cf77ee21-03a9-4954-ac25-9773a4cb27f4",
"type": "variant",
"text": [
"1855915"
],
"offsets": [
[
656,
663
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1855915"
}
]
},
{
"id": "f6bc1974-81b5-401c-8fca-7d83c5e9d44e",
"type": "variant",
"text": [
"1970244"
],
"offsets": [
[
667,
674
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1970244"
}
]
},
{
"id": "2581cd8f-aceb-4a3b-997f-7f12088fbac7",
"type": "variant",
"text": [
"538469"
],
"offsets": [
[
678,
684
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "538469"
}
]
},
{
"id": "540eec47-9779-4dc3-8c2e-a59f19eaa9de",
"type": "variant",
"text": [
"551266"
],
"offsets": [
[
688,
694
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "551266"
}
]
},
{
"id": "2cfe5524-fc59-4b3e-bbc9-ecca4f278a03",
"type": "variant",
"text": [
"489517"
],
"offsets": [
[
702,
708
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "489517"
}
]
}
] | [] | [] | [] |
30 | 14764791 | [
{
"id": "479440f6-a6d3-4d95-870e-ede175c4d2e0",
"type": "title",
"text": [
"Common variants in glutamine:fructose-6-phosphate amidotransferase 2 ( GFPT2 ) gene are associated with type 2 diabetes, diabetic nephropathy, and increased GFPT2 mRNA levels."
],
"offsets": [
[
0,
179
]
]
},
{
"id": "a47d80a8-01b8-4e6f-8723-681305f54683",
"type": "abstract",
"text": [
"Increased flux of glucose through the hexosamine biosynthetic pathway has been implicated in insulin resistance, altered insulin secretion, and diabetic nephropathy. Glutamine:fructose-6-phosphate amidotransferase (GFPT) , the rate limiting enzyme in hexosamine biosynthesis, is encoded by the unlinked but highly homologous genes GFPT1 and GFPT2 . We tested the hypothesis that GFPT2 sequence variation contributed to the susceptibility to type 2 diabetes mellitus (T2DM) and diabetic nephropathy in Caucasian and African-American individuals. We identified 11 single nucleotide polymorphisms (SNPs), of which seven were common. A single variant in exon 14, I471V , altered the amino acid sequence, is conserved between human and mouse genes, and was associated with T2DM among Caucasians (P = 0.05). A trend to an association was noted with diabetic nephropathy among African-American individuals (P = 0.15). Several variants in the 3' untranslated region (UTR) and exon 18 were also associated with T2DM in Caucasian individuals (P < 0.05), and the SNP in the 3' UTR was associated with diabetic nephropathy in African-American subjects (P = 0.047). GFPT2 mRNA levels in transformed lymphocytes from study subjects were significantly increased among African-American subjects compared with Caucasian individuals, regardless of diagnosis. Furthermore, the associated allele of the 3' UTR SNP was approximately 2-fold overexpressed. We propose that the 3' UTR variant results in increased GFPT2 mRNA levels with resultant increased hexosamine flux. The I471V variant may contribute to altered protein function or may simply be in linkage disequilibrium with the 3' UTR."
],
"offsets": [
[
180,
1867
]
]
}
] | [
{
"id": "591195b4-1322-4b34-904e-3716fbbfe0cf",
"type": "gene",
"text": [
"insulin"
],
"offsets": [
[
274,
281
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3630"
}
]
},
{
"id": "ea436d0d-cc9f-405e-bad8-41521d59f1a7",
"type": "gene",
"text": [
"insulin"
],
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[
274,
281
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3630"
}
]
},
{
"id": "042c1774-8c8e-484e-b81e-d24e6b263412",
"type": "gene",
"text": [
"Glutamine:fructose-6-phosphate amidotransferase (GFPT)"
],
"offsets": [
[
351,
405
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "29662c65-f4b6-4a77-a932-2817117bf7f4",
"type": "gene",
"text": [
"GFPT1"
],
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[
517,
522
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2673"
}
]
},
{
"id": "e478e2a7-6884-4ef7-ab7e-b10ec4d01478",
"type": "gene",
"text": [
"GFPT2"
],
"offsets": [
[
73,
78
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "247b8c55-b526-4aff-bf46-54d53004a442",
"type": "gene",
"text": [
"GFPT2"
],
"offsets": [
[
73,
78
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "d6c065a8-e315-4ae4-8fc9-a0d8bf304621",
"type": "gene",
"text": [
"GFPT2"
],
"offsets": [
[
73,
78
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "bb15db1f-d57f-4b59-98b4-2ccd350e37f5",
"type": "gene",
"text": [
"GFPT2"
],
"offsets": [
[
73,
78
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "482d56be-e5f1-4b85-abf1-76a4abe8796e",
"type": "variant",
"text": [
"I471V"
],
"offsets": [
[
850,
855
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2303007"
}
]
},
{
"id": "2da19cb8-2733-4218-a598-80c0910b0115",
"type": "variant",
"text": [
"I471V"
],
"offsets": [
[
850,
855
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2303007"
}
]
}
] | [] | [] | [] |
31 | 14871556 | [
{
"id": "58b6c2f3-70f0-4100-999e-d1f7302341ec",
"type": "title",
"text": [
"KCNJ11 polymorphisms and sudden cardiac death in patients with acute myocardial infarction."
],
"offsets": [
[
0,
92
]
]
},
{
"id": "c5225926-b19b-4416-9320-31c24294b3c1",
"type": "abstract",
"text": [
"PURPOSE: Patients with an acute myocardial infarction (AMI) are of high risk to develop ischemia-induced ventricular arrhythmias, leading to sudden cardiac death (SCD) in about one third of all AMI patients. The individual susceptibility to ischemia-induced arrhythmias may be modified by polymorphisms in genes encoding ion channels. The cardiac ATP-dependent potassium channel (K(ATP)) current is generated by ion channels encoded by the KCNJ11 gene and the SUR2a gene. Opening of the K(ATP) channel during ischemia results in action potential shortening in various studies and may therefore influence the outcome of AMI patients. METHODS: Using a three-primer strategy, we sequenced the complete coding and adjacent 5' and 3' sequences of the intronless KCNJ11 gene (1.3 kb) prospectively in two groups. Patients of group 1 (n = 84) survived three or more transmyocardial infarctions without developing any ventricular arrhythmias. Patients of group 2 died suddenly from their first myocardial infarction (n = 86), most of them witnessed SCDs. RESULTS: We identified a total of six known polymorphisms ( K23E , A190A , L267V , L270V , I337V , and K281K ) and two new polymorphisms ( L267L , 3'UTR +62 G/A ). The allele, genotype, and haplotype frequencies did not differ between the two groups. All polymorphisms were found to be in Hardy-Weinberg equilibrium. In addition, we identified two novel missense mutations in a highly conserved region of the gene in two patients of group 2 ( P266T and R371H ) with yet unknown functional consequences. CONCLUSION: In this study of AMI patients, SCD was not related to polymorphisms in the KCNJ11 gene."
],
"offsets": [
[
93,
1758
]
]
}
] | [
{
"id": "14fdd76a-c70b-475e-8fcf-92228ecf511b",
"type": "gene",
"text": [
"KCNJ11"
],
"offsets": [
[
0,
6
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3767"
}
]
},
{
"id": "460598ef-1edb-41c2-a8d7-80873ac3c756",
"type": "gene",
"text": [
"SUR2a"
],
"offsets": [
[
556,
561
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "10060"
}
]
},
{
"id": "1d4c56f1-2105-4ab3-9637-fd7b503a58b5",
"type": "gene",
"text": [
"KCNJ11"
],
"offsets": [
[
0,
6
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3767"
}
]
},
{
"id": "ff4187a6-e755-4a03-b9a9-f9f248b76c0d",
"type": "gene",
"text": [
"KCNJ11"
],
"offsets": [
[
0,
6
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3767"
}
]
},
{
"id": "21457bdf-09f6-45d5-94e5-be2a48b1c813",
"type": "variant",
"text": [
"K23E"
],
"offsets": [
[
1206,
1210
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5219"
}
]
},
{
"id": "af8f53d9-5561-48f3-a3a7-67a156e48289",
"type": "variant",
"text": [
"A190A"
],
"offsets": [
[
1214,
1219
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5218"
}
]
},
{
"id": "497adc07-d180-43f6-bd79-698a91838c85",
"type": "variant",
"text": [
"L267V"
],
"offsets": [
[
1223,
1228
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "L267V"
}
]
},
{
"id": "07aa494b-5333-4018-8fa5-608d1fc5bd88",
"type": "variant",
"text": [
"L270V"
],
"offsets": [
[
1232,
1237
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1800467"
}
]
},
{
"id": "1be05079-e1f8-4232-a248-c91b92d2155f",
"type": "variant",
"text": [
"I337V"
],
"offsets": [
[
1241,
1246
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5215"
}
]
},
{
"id": "2938acbd-dc01-44d6-ada7-67bed435ab57",
"type": "variant",
"text": [
"K281K"
],
"offsets": [
[
1254,
1259
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "K281K"
}
]
},
{
"id": "a285b1b2-3747-46d9-8242-feb7f49ce21a",
"type": "variant",
"text": [
"L267L"
],
"offsets": [
[
1290,
1295
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5216"
}
]
},
{
"id": "491ad0b2-57b9-4e6b-a6b2-f655610d8866",
"type": "variant",
"text": [
"3'UTR +62 G/A"
],
"offsets": [
[
1299,
1312
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G62A"
}
]
},
{
"id": "197d0625-933f-4a9b-8d27-d7569226fa79",
"type": "variant",
"text": [
"P266T"
],
"offsets": [
[
1595,
1600
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "P266T"
}
]
},
{
"id": "efe632f6-9212-4038-8972-d683a3db27b9",
"type": "variant",
"text": [
"R371H"
],
"offsets": [
[
1607,
1612
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "R371H"
}
]
}
] | [] | [] | [] |
32 | 14872030 | [
{
"id": "02470daf-ffbd-4ad9-84af-64051fb1261a",
"type": "title",
"text": [
"Functional MxA promoter polymorphism associated with subacute sclerosing panencephalitis."
],
"offsets": [
[
0,
91
]
]
},
{
"id": "9065d996-bfad-420f-a762-9d86a1f34a27",
"type": "abstract",
"text": [
"BACKGROUND: The antivirally active MxA protein is induced by interferon (IFN) alpha/beta and inhibits the replication of single-stranded RNA viruses including measles virus (MV). The authors investigated whether the MxA gene contributed to the development of subacute sclerosing panencephalitis (SSPE) in Japanese individuals. METHODS: Single-nucleotide polymorphisms (SNP) in the promoter region of the MxA gene were screened, association studies were performed between two SNP and SSPE, and then a functional difference in the promoter activities of the two SNP was investigated by a dual luciferase reporter assay. RESULTS: Four SNP were found ( -88 G/T , -123 C/A , -200 T/C , and -213 G/T ), and SSPE patients exhibited a higher frequency of both the -88T allele and the -88TT genotype than controls (p = 0.040 and 0.003). The IFN-induced up-regulation of the MxA promoter activity of the sequence with -88T was found to be significantly higher than that with G. CONCLUSIONS: MxA promoter -88 G/T SNP may confer host genetic susceptibility to SSPE in Japanese individuals. The finding that homozygotes of the MxA -88T allele with a high MxA -producing capability were more frequently seen in SSPE patients suggests that the MxA protein promotes the establishment of persistent MV infection of neural cells."
],
"offsets": [
[
92,
1423
]
]
}
] | [
{
"id": "f032e12d-f995-4701-9b96-289b4f50275e",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "9f7a30c7-9012-4e38-9992-f093e00f8264",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "7328531f-12cc-402c-8cfd-fd4191077b38",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "8d144ed8-67b4-41b7-b91e-09bb874e9a87",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "93d9ff46-0ed9-4164-be55-0c5988a10622",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "6fac7617-32a7-447c-8ff9-6a8a9c64af4c",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "d888caf1-a036-45f3-a363-f5683b4bdc73",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "bbeb5ade-19f8-475c-95e6-1a0ae4359344",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "e6f1ea94-7f0e-42b7-a8b8-b21ee4ab08c5",
"type": "variant",
"text": [
"-88 G/T"
],
"offsets": [
[
747,
754
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-88T"
}
]
},
{
"id": "e890f573-bb50-4585-8b01-d169a67ebcd6",
"type": "variant",
"text": [
"-123 C/A"
],
"offsets": [
[
758,
766
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-123A"
}
]
},
{
"id": "de7b7aa9-5fff-4f33-b59b-03516265a4a5",
"type": "variant",
"text": [
"-200 T/C"
],
"offsets": [
[
770,
778
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T-200C"
}
]
},
{
"id": "741bfced-64a1-44f3-b7ec-0f9c1af4e35a",
"type": "variant",
"text": [
"-213 G/T"
],
"offsets": [
[
786,
794
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-213T"
}
]
},
{
"id": "4a69c8e0-121c-42c3-85d0-8e43d74a0167",
"type": "variant",
"text": [
"-88 G/T"
],
"offsets": [
[
747,
754
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-88T"
}
]
}
] | [] | [] | [] |
33 | 14961571 | [
{
"id": "e5daca47-e7df-4c8f-8643-90ee6bb04752",
"type": "title",
"text": [
"-160C/A polymorphism in the E-cadherin gene promoter and risk of hereditary, familial and sporadic prostate cancer."
],
"offsets": [
[
0,
118
]
]
},
{
"id": "9666e576-c959-42ac-a172-01f0f2c40ac4",
"type": "abstract",
"text": [
"The E-cadherin (CDH1) gene has been associated with prostate carcinogenesis. The C/A polymorphism--160 base pairs relative to the transcription start site has been shown to decrease gene transcription. We analyzed the association between this polymorphism and the risk of sporadic, familial (2 close relatives) and hereditary (3 or more close relatives) prostate cancer. We combined data from 3 population-based epidemiologic studies in Sweden encompassing altogether 1,036 prostate cancer cases and 669 controls that were genotyped for the short nucleotide polymorphism. Odds ratios with 95% confidence intervals were estimated through unconditional logistic regression. We found no significant association between the A-allele and sporadic (OR = 1.0; 95% CI = 0.8-1.2) or familial (OR = 1.4; 95% CI = 0.9-2.2) prostate cancer. In contrast, risk of hereditary cancer was increased among heterozygote CA carriers (OR = 1.7; 95% CI = 1.0-2.7) and particularly among homozygote AA carriers (OR = 2.6; 95% CI = 1.4-4.9). Our data indicate that the -160 single nucleotide polymorphism in CDH1 is a low-penetrant prostate cancer susceptibility gene that might explain a proportion of familial and notably hereditary prostate cancer."
],
"offsets": [
[
119,
1350
]
]
}
] | [
{
"id": "7c8925dd-a0d1-4650-9086-3c91b6b08f47",
"type": "gene",
"text": [
"E-cadherin"
],
"offsets": [
[
30,
40
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "999"
}
]
},
{
"id": "11a32dcf-650a-44fc-a4c3-856f6b2e0d7a",
"type": "variant",
"text": [
"C/A polymorphism--160 base pairs relative to the transcription start site"
],
"offsets": [
[
203,
276
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-160A"
}
]
}
] | [] | [] | [] |
34 | 14961572 | [
{
"id": "29b88d37-ade0-4b72-ac71-be3459c495ac",
"type": "title",
"text": [
"Polymorphisms of the interleukin-1 beta gene are associated with increased risk of non-small cell lung cancer."
],
"offsets": [
[
0,
112
]
]
},
{
"id": "a7d6a9a3-a57f-48a9-adbe-d7bcb029dac4",
"type": "abstract",
"text": [
"Lung cancer is one of the leading causes of cancer death worldwide. Tobacco smoking is the main risk factor for lung cancer. Less than 20% of smokers develop lung cancer in their lifetime, however, indicating individual variations in lung cancer risk. Pro-inflammatory cytokines produced by inflammatory cells have been associated with inflammatory diseases and cancer. The IL1B gene, encoding IL-1beta cytokine, contains several single nucleotide polymorphisms (SNPs). Two of these are in the promoter region, at positions -511 (C-T) and -31 (T-C) . These polymorphisms have been associated with increased risk of developing a number of inflammatory diseases and gastric carcinoma. We genotyped the 2 polymorphisms in 251 non-small cell lung cancer patients from Norway and 272 healthy controls chosen from the general Norwegian population. The T allele at the -31 SNP (p = 0.01) and C allele at -511 SNP (p < 0.01) were over represented in lung cancer cases. The homozygote subjects were particularly at higher risk of lung cancer with odds ratio of 2.39 (95% CI = 1.29-4.44) for -31T/T and 2.51 (95% CI = 1.47-4.58) for -511C/C genotypes. In view of the significance of the p53 gene in lung carcinogenesis, we also analyzed the IL1B genotypes in relation to p53 mutations in the tumors. The results indicated that subjects having homozygote genotypes were more likely to have a mutation in the p53 gene (p = 0.05). This is the first study to provide evidence for an association of 1L1B gene polymorphisms with lung cancer risk."
],
"offsets": [
[
113,
1666
]
]
}
] | [
{
"id": "e993f6cc-ebae-4329-a8d4-3ae0f376ab48",
"type": "gene",
"text": [
"IL1B"
],
"offsets": [
[
488,
492
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3553"
}
]
},
{
"id": "d91fb3a5-952f-46a3-86b2-1524fa117b31",
"type": "gene",
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"IL-1beta"
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510,
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"db_id": "3553"
}
]
},
{
"id": "85de2741-d117-41c4-b4cf-9f987166a85f",
"type": "gene",
"text": [
"p53"
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1306,
1309
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"db_id": "7157"
}
]
},
{
"id": "ee26b33d-6b47-4add-bd80-777cacdfd89c",
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"IL1B"
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488,
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]
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{
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"p53"
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]
},
{
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"p53"
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1306,
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]
},
{
"id": "b2c71c3f-4e6f-4702-84e5-1d7c4619f7a9",
"type": "variant",
"text": [
"-511 (C-T)"
],
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[
642,
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]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-511T"
}
]
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{
"id": "75608be8-47cc-4478-a4ad-84e2e0022e87",
"type": "variant",
"text": [
"-31 (T-C)"
],
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[
659,
668
]
],
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{
"db_name": "dbSNP",
"db_id": "1143627"
}
]
},
{
"id": "74cc3652-5d33-4f4a-aa6c-db482b0d764c",
"type": "variant",
"text": [
"T allele at the -31 SNP"
],
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[
967,
990
]
],
"normalized": [
{
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"db_id": "1143627"
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]
},
{
"id": "6e31805f-95ca-4a53-99a7-84dea1ac2f0b",
"type": "variant",
"text": [
"C allele at -511 SNP"
],
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[
1008,
1028
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-511C"
}
]
},
{
"id": "bdb59a71-2136-4916-b171-afaddef28039",
"type": "variant",
"text": [
"-31T/T"
],
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1207,
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]
],
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"db_id": "1143627"
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]
},
{
"id": "4bb11f7e-f155-44c7-8468-72c2291dfade",
"type": "variant",
"text": [
"-511C/C"
],
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1250,
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]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-511C"
}
]
}
] | [] | [] | [] |
35 | 14962090 | [
{
"id": "2f81e8b5-7a81-45cf-af8a-c86e64559192",
"type": "title",
"text": [
"Evaluation of the IRF-2 gene as a candidate for PSORS3 ."
],
"offsets": [
[
0,
59
]
]
},
{
"id": "b650eebb-c339-404b-bb72-caec3b3efdca",
"type": "abstract",
"text": [
"Type 1 interferon can trigger flares of psoriasis. Hypersensitivity to type 1 interferon signaling causes a psoriasis-like skin disease in mice deficient for the transcription factor interferon regulatory factor 2 (IRF2). The human IRF2 gene is located at a previously identified candidate psoriasis susceptibility locus on chromosome 4q ( PSORS3 at D4S1535). Therefore, we tested association of psoriasis with IRF2. We generated a sample consisting of 157 families with a total of 521 individuals. Five novel microsatellite markers were developed and typed, and complemented with three known markers to yield a set of eight markers spaced within 600 kb around the IRF2 gene, three of which are located in the gene. We detected association of IRF2 with type 1 psoriasis at two markers in the IRF2 gene. Haplotype sharing analysis confirmed association of IRF2 with type 1 psoriasis (p=0.0017; pcorr=0.03). The 921G/A SNP in exon 9 was found to obliterate a predicted exon splice enhancer in an allele-specific manner. There was a suggestive increase of homozygosity for the splicing-deficient allele in type 1 psoriasis patients. Our data identify IRF2 as a potential susceptibility gene for psoriasis."
],
"offsets": [
[
60,
1265
]
]
}
] | [
{
"id": "0f3b7642-de09-4db1-8bac-dca4f470721d",
"type": "gene",
"text": [
"PSORS3"
],
"offsets": [
[
51,
57
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7889"
}
]
},
{
"id": "4cd3cb31-d04f-48c8-ad45-5d28aaa80498",
"type": "variant",
"text": [
"921G/A "
],
"offsets": [
[
972,
979
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G921A"
}
]
}
] | [] | [] | [] |
36 | 14962947 | [
{
"id": "e55ad154-2de0-4942-a346-b37492cfbde6",
"type": "title",
"text": [
"In-depth haplotype analysis of ABCA1 gene polymorphisms in relation to plasma ApoA1 levels and myocardial infarction."
],
"offsets": [
[
0,
121
]
]
},
{
"id": "42f5a3a9-5d68-4aa4-b313-7f8714e08415",
"type": "abstract",
"text": [
"OBJECTIVE: By regulating the cellular cholesterol efflux from peripheral cells to high-density lipoprotein, the ABCA1 protein is suspected to play a key role in lipid homeostasis and atherosclerosis. Twenty-six polymorphisms of the ABCA1 gene were genotyped and tested for association with plasma levels of ApoA1 and myocardial infarction (MI) in the ECTIM study. METHODS AND RESULTS: In addition to single-locus analysis, a systematic exploration of all possible haplotype effects was performed, with this exploration being performed on a minimal set of \"tag\" polymorphisms that define the haplotype structure of the gene. Two polymorphisms were associated with plasma levels of ApoA1 , 1 in the promoter ( C-564T ) and 1 in the coding ( R1587K ) regions, whereas only 1 polymorphism ( R219K ) was associated with the risk of MI. However, no haplotype effect was detected on ApoA1 variability or on the risk of MI. CONCLUSIONS: ABCA1 gene polymorphisms but not haplotypes are involved in the variability of plasma ApoA1 and the susceptibility to coronary artery disease."
],
"offsets": [
[
122,
1206
]
]
}
] | [
{
"id": "8407fa01-c4a9-490c-91c1-483fa91b757f",
"type": "gene",
"text": [
"ABCA1"
],
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[
32,
37
]
],
"normalized": [
{
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"db_id": "19"
}
]
},
{
"id": "b46306c4-8a09-4965-b2b0-6b42341c588c",
"type": "gene",
"text": [
"ABCA1"
],
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32,
37
]
],
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}
]
},
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"id": "34a8e66f-7d33-4916-a413-da582652111d",
"type": "gene",
"text": [
"ApoA1"
],
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81,
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]
],
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"db_id": "335"
}
]
},
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"id": "3120cb13-51c6-4847-89a0-a78cd7791cb3",
"type": "gene",
"text": [
"ApoA1"
],
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81,
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]
],
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}
]
},
{
"id": "3f933ae3-f459-4b8c-949d-a91d4b03b136",
"type": "gene",
"text": [
"ApoA1"
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81,
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],
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]
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"id": "6f649411-e0a6-4e69-b421-759ece234fc8",
"type": "gene",
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"ABCA1"
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32,
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]
],
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"db_id": "19"
}
]
},
{
"id": "32674c48-e6fd-4bbb-834c-1ff21b8525da",
"type": "gene",
"text": [
"ApoA1"
],
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81,
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]
],
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"db_id": "335"
}
]
},
{
"id": "c542a7d0-d8b1-447c-9c82-99d7fc848ef4",
"type": "variant",
"text": [
"C-564T"
],
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[
837,
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]
],
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{
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"db_id": "C-564T"
}
]
},
{
"id": "6048ac19-634a-4c42-9068-e50fa3b3faf1",
"type": "variant",
"text": [
"R1587K"
],
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[
868,
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]
],
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{
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"db_id": "2230808"
}
]
},
{
"id": "15727abc-e819-45b8-a0ed-6dc645d8e04c",
"type": "variant",
"text": [
"R219K"
],
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[
916,
921
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2230806"
}
]
}
] | [] | [] | [] |
37 | 14970360 | [
{
"id": "11deea42-5057-47d5-b026-eb8baa9ddd54",
"type": "title",
"text": [
"Three single-nucleotide polymorphisms of the angiotensinogen gene and susceptibility to hypertension: single locus genotype vs. haplotype analysis."
],
"offsets": [
[
0,
149
]
]
},
{
"id": "08795029-000e-4a1b-9f68-c5bc19af0e1c",
"type": "abstract",
"text": [
"Although some single polymorphism analyses of the angiotensinogen ( AGT ) gene have been found to be associated with hypertension, the results are still inconsistent. The objectives of this study are to evaluate the association of the genotype and haplotype distributions of three single-nucleotide polymorphisms (SNPs) ( G-217A , A-6G , and M235T ) in the AGT gene with hypertension. In a sample of 461 hypertensive and 327 normotensive patients in Taiwan, we found that -217AA and -6GG homozygotes conferred independently an increased risk to hypertension (P = 0.008 and P = 0.037, respectively), as illustrated by their significant associations with hypertension in both single SNP and pair-wise SNPs analyses. Meanwhile, a very weak linkage disequilibrium was found between the G-217A and the A-6G polymorphisms in terms of r2 (<0.05). On the basis of likelihood ratio test, only the set of haplotypes that constituted the A-6G and the M235T polymorphisms was associated with hypertension (chi2 = 20.91, P = 0.0008), which was mainly due to the increased frequency of the recombinant haplotypes ( -6A identical with 235M and -6G identical with 235T), and a pathophysiological role in the predisposition to hypertension was hence indicated. In functional assays, the promoter activities of the haplotypes -217A identical with -6A and -217G identical with -6G were significantly higher than the most common haplotype -217G identical with -6A . These results highlight the necessity of a thorough analysis of all reported variants of a candidate gene in the elucidation of genetic susceptibility to a complex disease like hypertension, even when the variants are in the same haplotype block."
],
"offsets": [
[
150,
1874
]
]
}
] | [
{
"id": "a8fb5dcc-3c11-4b16-ab49-6515d95fde0c",
"type": "gene",
"text": [
"angiotensinogen"
],
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[
46,
61
]
],
"normalized": [
{
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"db_id": "183"
}
]
},
{
"id": "1d4ec668-d9e4-4d05-966c-8d29aa5e7057",
"type": "gene",
"text": [
"AGT"
],
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[
220,
223
]
],
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}
]
},
{
"id": "5b925983-e8b4-421e-83a5-887c8d06d4eb",
"type": "gene",
"text": [
"AGT"
],
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220,
223
]
],
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}
]
},
{
"id": "c87149e6-1438-4fb9-816a-7988b399d4ff",
"type": "variant",
"text": [
"G-217A"
],
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474,
480
]
],
"normalized": [
{
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"db_id": "G-217A"
}
]
},
{
"id": "4566dd17-2a4a-4f50-a7cc-22fca19de4bb",
"type": "variant",
"text": [
"A-6G"
],
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[
484,
488
]
],
"normalized": [
{
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"db_id": "A-6G"
}
]
},
{
"id": "4b49c284-a4ce-4444-91d3-217f205e5a13",
"type": "variant",
"text": [
"M235T"
],
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496,
501
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "M235T"
}
]
},
{
"id": "7bb89bb5-967b-4d04-980f-7e21f40a4c42",
"type": "variant",
"text": [
"-217AA"
],
"offsets": [
[
629,
635
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-217A"
}
]
},
{
"id": "47dcc37e-64a3-4a0d-a298-83111f7156f6",
"type": "variant",
"text": [
"-6GG"
],
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642,
646
]
],
"normalized": [
{
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"db_id": "G-6G"
}
]
},
{
"id": "88f1c7f1-e4d3-459f-905e-88bbdcc80400",
"type": "variant",
"text": [
"G-217A"
],
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474,
480
]
],
"normalized": [
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"db_id": "G-217A"
}
]
},
{
"id": "22e49c89-e010-4693-9450-fa1d9a163786",
"type": "variant",
"text": [
"A-6G"
],
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484,
488
]
],
"normalized": [
{
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"db_id": "A-6G"
}
]
},
{
"id": "d2e43016-7747-4453-b343-db676b47bb24",
"type": "variant",
"text": [
"A-6G"
],
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484,
488
]
],
"normalized": [
{
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"db_id": "A-6G"
}
]
},
{
"id": "0897c50f-a20f-42cb-b06d-9be386ffc5ff",
"type": "variant",
"text": [
"M235T"
],
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496,
501
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "M235T"
}
]
},
{
"id": "9bc4d80f-048d-4db0-954c-4a404f20a7c8",
"type": "variant",
"text": [
"-6A"
],
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[
1269,
1272
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-6A"
}
]
},
{
"id": "064f5cd4-cd13-4351-9967-fbe8f9df04bf",
"type": "variant",
"text": [
"-6G"
],
"offsets": [
[
485,
488
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-6G"
}
]
},
{
"id": "e18d6286-ce08-41ff-aebe-995545b4f8e7",
"type": "variant",
"text": [
"-217A"
],
"offsets": [
[
475,
480
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-217A"
}
]
},
{
"id": "72564ad9-fa82-4880-9454-c5f1be89b19e",
"type": "variant",
"text": [
"-6A"
],
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1269,
1272
]
],
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{
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"db_id": "-6A"
}
]
},
{
"id": "986c7898-a440-4856-84ba-90593ca0a66b",
"type": "variant",
"text": [
"-217G"
],
"offsets": [
[
1513,
1518
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-217G"
}
]
},
{
"id": "5ca1cd8b-7b98-4cab-af60-92bab5d45fea",
"type": "variant",
"text": [
"-6G"
],
"offsets": [
[
485,
488
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-6G"
}
]
},
{
"id": "cec6d24c-78c4-417d-a705-0422d5e2508b",
"type": "variant",
"text": [
"-217G"
],
"offsets": [
[
1513,
1518
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-217G"
}
]
},
{
"id": "932432d6-80e7-4c1a-a244-ced3983df3ac",
"type": "variant",
"text": [
"-6A"
],
"offsets": [
[
1269,
1272
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-6A"
}
]
}
] | [] | [] | [] |
38 | 14970363 | [
{
"id": "37baa1f1-70df-4026-8b27-7e65235c2007",
"type": "title",
"text": [
"Tests of linkage and/or association of the LEPR gene polymorphisms with obesity phenotypes in Caucasian nuclear families."
],
"offsets": [
[
0,
123
]
]
},
{
"id": "ca9b2d85-4da9-40ba-90c6-4cc63de07efa",
"type": "abstract",
"text": [
"Genetic variations in the leptin receptor ( LEPR ) gene have been conceived to affect body weight in general populations. In this study, using the tests implemented in the statistical package QTDT, we evaluated association and/or linkage of the LEPR gene with obesity phenotypes in a large sample comprising 1,873 subjects from 405 Caucasian nuclear families. Obesity phenotypes tested include body mass index (BMI), fat mass, percentage fat mass (PFM), and lean mass, with the latter three measured by dual-energy X-ray absorptiometry (DXA). Three single nucleotide polymorphisms (SNPs), namely Lys109Arg (A/G) , Lys656Asn (G/C) , Pro1019Pro (G/A) , in the LEPR gene were analyzed. Significant linkage disequilibrium (0.394 < or = |D'| < or = 0.688, P < 0.001) was observed between pairs of the three SNPs. No significant population stratification was found for any SNP/phenotype. In single-locus analyses, evidence of association was observed for Lys656Asn with lean mass (P = 0.002) and fat mass (P = 0.015). The contribution of this polymorphism to the phenotypic variation of lean mass and fat mass was 2.63% and 1.15%, respectively. Subjects carrying allele G at the Lys656Asn site had, on average, 3.16% higher lean mass and 2.71% higher fat mass than those without it. In the analyses for haplotypes defined by the three SNPs, significant associations were detected between haplotype GCA (P = 0.005) and lean mass. In addition, marginally significant evidence of association was observed for this haplotype with fat mass (P = 0.012). No statistically significant linkage was found, largely due to the limited power of the linkage approach to detect small genetic effects in our data sets. Our results suggest that the LEPR gene polymorphisms contribute to variation in obesity phenotypes."
],
"offsets": [
[
124,
1935
]
]
}
] | [
{
"id": "4ed6c30a-4a63-45a3-b055-8f73ef698547",
"type": "gene",
"text": [
"leptin receptor"
],
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[
151,
166
]
],
"normalized": [
{
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}
]
},
{
"id": "ef6f835e-347f-4b36-a6f1-7cbe13bbbe8d",
"type": "gene",
"text": [
"LEPR"
],
"offsets": [
[
44,
48
]
],
"normalized": [
{
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"db_id": "3953"
}
]
},
{
"id": "0161619f-1f8d-4651-b90d-225f473f47ab",
"type": "gene",
"text": [
"LEPR"
],
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[
44,
48
]
],
"normalized": [
{
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"db_id": "3953"
}
]
},
{
"id": "01416876-0b69-41c6-8b43-d27f07ba189d",
"type": "gene",
"text": [
"LEPR"
],
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[
44,
48
]
],
"normalized": [
{
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}
]
},
{
"id": "5a3978af-b5d4-4bff-ae0a-26ec86cf1e53",
"type": "gene",
"text": [
"LEPR"
],
"offsets": [
[
44,
48
]
],
"normalized": [
{
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"db_id": "3953"
}
]
},
{
"id": "a82a9df9-c538-4a47-8036-861d446532e9",
"type": "variant",
"text": [
"Lys109Arg (A/G)"
],
"offsets": [
[
725,
740
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1137100"
}
]
},
{
"id": "3a9af473-b582-4736-9697-84feaa3ef0fa",
"type": "variant",
"text": [
"Lys656Asn (G/C)"
],
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[
744,
759
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "8179183"
}
]
},
{
"id": "01df9e1c-5e71-435f-8bd2-f9984cb411ce",
"type": "variant",
"text": [
"Pro1019Pro (G/A)"
],
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[
763,
779
]
],
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}
]
},
{
"id": "61dafa2c-7b04-4f4f-823f-8ba15001895d",
"type": "variant",
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"Lys656Asn"
],
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]
],
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}
]
},
{
"id": "ff669c7a-e021-49d8-a031-e17098ad3540",
"type": "variant",
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"Lys656Asn"
],
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744,
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]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "8179183"
}
]
}
] | [] | [] | [] |
39 | 14970845 | [
{
"id": "5e624c83-2f60-4c71-8ac1-d8fabaafde3e",
"type": "title",
"text": [
"Polymorphisms in the prion protein gene and in the doppel gene increase susceptibility for Creutzfeldt-Jakob disease."
],
"offsets": [
[
0,
121
]
]
},
{
"id": "e1ba8a65-52ee-4ca2-876c-c43e8ac8134d",
"type": "abstract",
"text": [
"The prion protein gene ( PRNP ) plays a central role in the origin of Creutzfeldt-Jakob disease (CJD), but there is growing interest in other polymorphisms that may be involved in CJD. Polymorphisms upstream of PRNP that may modulate the prion protein production as well as polymorphisms in the prion-like doppel gene ( PRND ) have been studied, with inconsistent findings. We investigated the role of a single-nucleotide polymorphism ( SNP 1368 ) located upstream of PRNP and three polymorphisms in PRND ( T26M , P56L and T174M ) in CJD. The study included a population-based sample of 52 patients with sporadic CJD and 250 controls. We analysed our data as single markers and haplotypes. Further, we conducted a meta-analysis on PRND T174M comparing the data of the four studies conducted to date. For SNP 1368 and PRNP M129V , we found significant evidence for linkage disequilibrium. No evidence was found for a relation of SNP 1368 to CJD independent of PRNP M129V . We further found a significant increased prevalence of M homozygotes at PRND T174M among sporadic CJD patients, when adjusting the analyses for the other genotypes. In the haplotype analyses, the association was strongest for persons homozygous for PRNP 129M and PRND 174M (odds ratio 4.35, 95% confidence interval 1.05-8.09; P=0.04). The meta-analysis on the PRND T174M polymorphism did not show a consistent effect across studies, raising the question as to whether PRND 174M is causally related to CJD, or whether the PRND allele is in linkage disequilibrium with another polymorphism related to CJD."
],
"offsets": [
[
122,
1748
]
]
}
] | [
{
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"prion protein gene"
],
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22,
40
]
],
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}
]
},
{
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"PRNP"
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149,
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]
},
{
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"PRNP"
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149,
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]
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"prion protein"
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22,
35
]
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}
]
},
{
"id": "2afba729-d85f-44bc-8627-6218c398bcf9",
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"prion-like doppel gene"
],
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424,
446
]
],
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"db_id": "23627"
}
]
},
{
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"PRND"
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450,
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]
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}
]
},
{
"id": "a14ee03c-2065-4cce-b399-598fdec556bc",
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"PRNP"
],
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149,
153
]
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}
]
},
{
"id": "ed9f3b32-14d3-41f5-9bc4-c5003a55fd4a",
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"PRND"
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450,
454
]
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}
]
},
{
"id": "2f3b5003-e6aa-47af-abc2-243320c56d29",
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"PRND"
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450,
454
]
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}
]
},
{
"id": "d1dcba35-634d-4e88-a643-72836be38695",
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"PRNP"
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149,
153
]
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]
},
{
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149,
153
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}
]
},
{
"id": "30b425bf-3390-47fc-be2c-70dfc5050c7a",
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450,
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]
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{
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149,
153
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}
]
},
{
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450,
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},
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"id": "92bff42e-2af2-492b-8859-673032cfad37",
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450,
454
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]
},
{
"id": "dd42e7df-2d4e-4f81-98d9-185f1db90b7a",
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"PRND"
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450,
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]
},
{
"id": "013365a2-92f7-48ce-81bf-fbe56edd60d2",
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"PRND"
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450,
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}
]
},
{
"id": "15f203f0-b207-4833-a407-856427c84cf7",
"type": "variant",
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"SNP 1368"
],
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567,
575
]
],
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}
]
},
{
"id": "4d021d0d-14ff-4476-83cd-4efd897ded77",
"type": "variant",
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"T26M"
],
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641,
645
]
],
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"db_id": "T26M"
}
]
},
{
"id": "79dffd15-ef5d-4265-810c-c940099ef778",
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"P56L"
],
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649,
653
]
],
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}
]
},
{
"id": "b14507b9-58dd-4c94-a56d-27aafd053033",
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"T174M"
],
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660,
665
]
],
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}
]
},
{
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"type": "variant",
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"T174M"
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660,
665
]
],
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}
]
},
{
"id": "02e61bc3-ca33-4f50-a77e-072a8199a8e2",
"type": "variant",
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"SNP 1368"
],
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567,
575
]
],
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}
]
},
{
"id": "b99f0620-9ebd-4ac3-b457-b72b74ace11b",
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"M129V"
],
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968,
973
]
],
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}
]
},
{
"id": "924c7e46-9802-4186-bcd3-b39846d3b9ff",
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567,
575
]
],
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}
]
},
{
"id": "884a0008-81d6-40bc-a092-f19a698f13a8",
"type": "variant",
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"M129V"
],
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968,
973
]
],
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}
]
},
{
"id": "eb2de92d-9448-45f7-8212-de9c298a9546",
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"T174M"
],
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660,
665
]
],
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"db_id": "2245220"
}
]
},
{
"id": "3a4d8011-2810-4905-a1f7-a786cc7b15a2",
"type": "variant",
"text": [
"129M"
],
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[
1384,
1388
]
],
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{
"db_name": "dbSNP",
"db_id": "1799990"
}
]
},
{
"id": "fa0f6958-a125-49a5-9900-7ff1856dfbbd",
"type": "variant",
"text": [
"174M"
],
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[
661,
665
]
],
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"db_id": "2245220"
}
]
},
{
"id": "aa223154-fd60-459b-9948-ff5ba38c3190",
"type": "variant",
"text": [
"T174M"
],
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660,
665
]
],
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"db_id": "2245220"
}
]
},
{
"id": "5974442f-4dd5-4adc-a375-c4cee16dc250",
"type": "variant",
"text": [
"174M"
],
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[
661,
665
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2245220"
}
]
}
] | [] | [] | [] |
40 | 14973548 | [
{
"id": "12d8b008-fae3-4864-9c41-2c895b0a9b9f",
"type": "title",
"text": [
"Is there a future for TNF promoter polymorphisms?"
],
"offsets": [
[
0,
51
]
]
},
{
"id": "bec64891-6f01-4367-80cb-9ac857ddcc8b",
"type": "abstract",
"text": [
"The in vitro study of TNF promoter polymorphism (SNP) function was stimulated by the numerous case-control (association) studies of the polymorphisms in relation to human disease and the appearance of several studies claiming to show a functional role for these SNPs provided a further impetus to researchers interested in the role of TNF in their disease of interest. In this review we consider case-control studies, concentrating on the autoimmune and inflammatory diseases rheumatoid arthritis, multiple sclerosis, ankylosing spondylitis, and asthma, and on infectious diseases including malaria, hepatitis B and C infection, leprosy and sepsis/septic shock. We also review the available evidence on the functional role of the various TNF promoter polymorphisms. In general, case-control studies have produced mixed results, with little consensus in most cases on whether any TNF polymorphisms are actually associated with disease, although results have been more consistent in the case of infectious diseases, particularly malaria. Functional studies have also produced mixed results but recent work suggests that the much studied -308G/A polymorphism is not functional, while the function of other TNF polymorphisms remains controversial. Studies of the TNF region are increasingly using extended haplotypes that can better capture the variation of the MHC region."
],
"offsets": [
[
52,
1435
]
]
}
] | [
{
"id": "4b9f7980-5644-4f59-802e-7683705ed369",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "f1dfb0fc-70d7-493e-be0e-649486dc905f",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
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"db_name": "NCBI Gene",
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}
]
},
{
"id": "8b349363-8c67-4a3a-a022-a4f8789eb7e4",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
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}
]
},
{
"id": "5bf644b6-3ffd-4a4e-9f3f-169c8f31643f",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
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}
]
},
{
"id": "442fc22a-6c9f-4385-87e5-2cc23e850f69",
"type": "gene",
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"TNF"
],
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[
23,
26
]
],
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}
]
},
{
"id": "4c804686-9506-4678-a842-11ac735d9602",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "29463222-1264-4fcd-b12f-4c81ed1c66ec",
"type": "variant",
"text": [
"-308G/A"
],
"offsets": [
[
1196,
1203
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-308A"
}
]
}
] | [] | [] | [] |
41 | 14973783 | [
{
"id": "d25db1e8-e142-4440-9bb8-3ac8bfc48829",
"type": "title",
"text": [
"Melanocortin-4 receptor gene variant I103 is negatively associated with obesity."
],
"offsets": [
[
0,
83
]
]
},
{
"id": "d52006e2-8f4f-41d7-b000-75348fe8f57d",
"type": "abstract",
"text": [
"Several rare mutations in the melanocortin-4 receptor gene (MC4R) predispose to obesity. For the most common missense variant V103I (rs2229616) , however, the previously reported similar carrier frequencies in obese and nonobese individuals are in line with in vitro studies, which have not shown a functional implication of this variant. In the present study, we initially performed a transmission/disequilibrium test on 520 trios with obesity, and we observed a lower transmission rate of the I103 allele (P=.017), which was an unexpected finding. Therefore, we initiated two large case-control studies (N=2,334 and N=661) and combined the data with those from 12 published studies, for a total of 7,713 individuals. The resulting meta-analysis provides evidence for a negative association of the I103 allele with obesity (odds ratio 0.69; 95% confidence interval 0.50-0.96; P=.03), mainly comprising samples of European origin. Additional screening of four other ethnic groups showed comparable I103 carrier frequencies well below 10%. Genomic sequencing of the MC4R gene revealed three polymorphisms in the noncoding region that displayed strong linkage disequilibrium with V103I. In our functional in vitro assays, the variant was indistinguishable from the wild-type allele, as was the result in previous studies. This report on an SNP/haplotype that is negatively associated with obesity expands the successful application of meta-analysis of modest effects in common diseases to a variant with a carrier frequency well below 10%. The respective protective effect against obesity implies that variation in the MC4R gene entails both loss and gain of function."
],
"offsets": [
[
84,
1759
]
]
}
] | [
{
"id": "c9a6c41b-219f-424f-9ab9-fe61fd31c76a",
"type": "gene",
"text": [
"melanocortin-4 receptor gene (MC4R)"
],
"offsets": [
[
115,
150
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "82820722-67fb-4c64-a2e6-90342304d5a3",
"type": "variant",
"text": [
"V103I (rs2229616)"
],
"offsets": [
[
213,
230
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
},
{
"id": "05654246-221f-4ce5-b692-85eeb5448c7f",
"type": "variant",
"text": [
"I103"
],
"offsets": [
[
39,
43
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
},
{
"id": "19f0ea71-ac52-46d0-9b06-c269bed02709",
"type": "variant",
"text": [
"I103"
],
"offsets": [
[
39,
43
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
},
{
"id": "243555a0-fc10-4c2e-9f97-b5a83373abb5",
"type": "variant",
"text": [
"I103"
],
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[
39,
43
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
}
] | [] | [] | [] |
42 | 14975928 | [
{
"id": "b8e83b12-1e5a-4309-9728-a4e75a03bea6",
"type": "title",
"text": [
"Molecular and functional characterization of common polymorphisms in HERG (KCNH2) ) potassium channels."
],
"offsets": [
[
0,
104
]
]
},
{
"id": "d91b6872-f987-4c97-8e64-d03c48f66a11",
"type": "abstract",
"text": [
"Long QT syndrome (LQTS) is a cardiac repolarization disorder that can lead to arrhythmias and sudden death. Chromosome 7-linked inherited LQTS (LQT2) is caused by mutations in human ether-a-go-go-related gene ( HERG ; KCNH2 ), whereas drug-induced LQTS is caused primarily by HERG channel block. Many common polymorphisms are functionally silent and have been traditionally regarded as benign and without physiological consequence. However, the identification of common nonsynonymous single nucleotide polymorphisms (nSNPs; i.e., amino-acid coding variants) with functional phenotypes in the SCN5A Na(+) channel and MiRP1 K(+) channel beta-subunit have challenged this viewpoint. In this report, we test the hypothesis that common missense HERG polymorphisms alter channel physiology. Comprehensive mutational analysis of HERG was performed on genomic DNA derived from a population-based cohort of sudden infant death syndrome and two reference allele cohorts derived from 100 African American and 100 Caucasian individuals. Amino acid-encoding variants were considered common polymorphisms if they were present in at least two of the three study cohorts with an allelic frequency >0.5%. Four nSNPs were identified: K897T , P967L , R1047L , and Q1068R . Wild-type (WT) and polymorphic channels were heterologously expressed in human embryonic kidney cells, and biochemical and voltage-clamp techniques were used to characterize their functional properties. All channel types were processed similarly, but several electrophysiological differences were identified: 1) K897T current density was lower than the other polymorphic channels; 2) K897T channels activated at more negative potentials than WT and R1047L ; 3) K897T and Q1068R channels inactivated and recovered from inactivation faster than WT, P967L , and R1047L channels; and 4) K897T channels showed subtle differences compared with WT channels when stimulated with an action potential waveform. In contrast to K897T and Q1068R channels, P967L and R1047L channels were electrophysiologically indistinguishable from WT channels. All HERG channels had similar sensitivity to block by cisapride. Therefore, some HERG polymorphic channels are electrophysiologically different from WT channels."
],
"offsets": [
[
105,
2390
]
]
}
] | [
{
"id": "25dd7fe5-b936-4a98-ab61-cfa6ba0f338d",
"type": "gene",
"text": [
"HERG"
],
"offsets": [
[
70,
74
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3757"
}
]
},
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{
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]
}
] | [] | [] | [] |
43 | 14979495 | [
{
"id": "f8683426-8805-469e-aa9b-9990da521bdc",
"type": "title",
"text": [
"The Arg753GLn polymorphism of the human toll-like receptor 2 gene in tuberculosis disease."
],
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0,
94
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{
"id": "e6b65436-1e48-4e4b-9133-f1eb0a3bb835",
"type": "abstract",
"text": [
"Toll-like receptor 2 (TLR2) TLR2 ), a member of the Toll-like receptor family, plays an important role in recognition of, and subsequent immune response activation against, mycobacteria. The genetic polymorphism of TLR2 ( arginine to glutamine substitution at residue 753 ( Arg753Gln )) has been associated with a negative influence on TLR2 function, which may, in turn, determine the innate host response to mycobacteria. The aim of the present study was to investigate the Arg753Gln single nucleotide polymorphism of the TLR2 gene in tuberculosis (TB) patients compared to healthy controls. A retrospective case/control study was carried out. The Arg753Gln polymorphism of the TLR2 gene was studied in 151 TB patients compared to 116 ethnically and age-matched healthy control subjects. The TLR2 polymorphism (adenine (A) allele) was observed in 17.9 and 7.7% of TB patients and controls, respectively. When the ratios of the three genotypes were compared between the two groups, the AA genotype was found to be more significantly associated with TB. Allele frequencies for guanine (G) and A were found to be 0.95 and 0.05 in the control group and 0.86 and 0.14 in the TB patient group, respectively. The risk of developing TB disease was increased 6.04- and 1.60-fold for carriers of the AA and GA genotypes, respectively. In conclusion, the present data suggest that the arginine to glutamine substitution at residue 753 polymorphism of the Toll-like receptor 2 gene influences the risk of developing tuberculosis."
],
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[
95,
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]
]
}
] | [
{
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]
},
{
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"arginine to glutamine substitution at residue 753"
],
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],
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]
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{
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{
"id": "e61c8182-4af1-46b7-8e9c-96650aed256d",
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"arginine to glutamine substitution at residue 753"
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]
}
] | [] | [] | [] |
44 | 14986114 | [
{
"id": "ff0cef8d-c475-4e96-a012-b88349d15ab8",
"type": "title",
"text": [
"A single nucleotide polymorphism in the MMP-1 promoter is correlated with histological differentiation of gastric cancer."
],
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[
0,
123
]
]
},
{
"id": "f91062e5-2373-40fb-9d18-1beb52e42747",
"type": "abstract",
"text": [
"PURPOSE: Matrix metalloproteinase-1 ( MMP-1 ) plays a key role in cancer invasion and metastasis by degradation of extracellular matrix (ECM) and basement membrane barriers. The 1G/2G single nucleotide polymorphism (SNP) in the MMP-1 promoter at position -1607 bp has been reported to affect the transcriptional activity. In the light of these findings, we investigated whether this SNP in the MMP-1 promoter is associated with the development, differentiation, and progression of gastric cancer. METHODS: The 215 gastric cancer patients and 166 controls were used in this study. The SNP of the MMP-1 promoter was analyzed by PCR-RFLP and sequencing. The genotype frequency was compared between cases and controls, and the association with clinicopathological parameters among cases was studied. RESULTS: The frequency of 1G/2G genotypes in gastric cancer patients was similar to those in controls (p=0.57). The degree of tumor invasion, the presence of lymph node metastasis, and clinical stage showed no significant association with the SNP. On the other hand, we found a significant association with histological differentiation and gender among gastric cancer patients (p<0.05, respectively). CONCLUSIONS: The presence of 2G allele in the MMP-1 promoter did not enhance the risk of gastric cancer; however, it may be involved in differentiation of gastric cancer."
],
"offsets": [
[
124,
1501
]
]
}
] | [
{
"id": "8b52b6d3-b863-4b86-a4ec-19717d63fa8d",
"type": "gene",
"text": [
"Matrix metalloproteinase-1"
],
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134,
160
]
],
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"db_id": "4312"
}
]
},
{
"id": "af7bc839-ffa6-4cf6-a231-851e3713ca94",
"type": "gene",
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41,
46
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],
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]
},
{
"id": "316b61b0-e792-41e0-b553-2e4f57885dba",
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"MMP-1"
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41,
46
]
],
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]
},
{
"id": "1bc775dc-f7c2-4873-9746-4ba5c8982e2f",
"type": "gene",
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"MMP-1"
],
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41,
46
]
],
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]
},
{
"id": "8e5d56b5-7cdd-404d-b61e-559cc22e8d44",
"type": "gene",
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"MMP-1"
],
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41,
46
]
],
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}
]
},
{
"id": "2ffbb9c0-64ba-40e4-a794-feb3e145e8b7",
"type": "variant",
"text": [
"1G/2G single nucleotide polymorphism (SNP) in the MMP-1 promoter at position -1607 bp"
],
"offsets": [
[
305,
390
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
}
] | [] | [] | [] |
45 | 14986169 | [
{
"id": "3d16e7b5-139f-47c6-a620-7ff60c1bb06e",
"type": "title",
"text": [
"Association of the T-cell regulatory gene CTLA4 with Graves' disease and autoimmune thyroid disease in the Japanese."
],
"offsets": [
[
0,
118
]
]
},
{
"id": "aab3d27b-502a-476c-a424-42554c09f768",
"type": "abstract",
"text": [
"Autoimmune thyroid disease (AITD) is caused by an immune response to self-thyroid antigen. The cytotoxic T-lymphocyte antigen-4 ( CTLA4 ) gene, encoding a negative regulator of the T-lymphocyte immune response, had been reported to be associated and/or linked to AITD. Recently, AITD susceptibility in the Caucasians was mapped to the 6.1-kb 3'UTR of the CTLA4 gene, in which the three single-nucleotide polymorphisms (SNPs) CT60 , JO31 , and JO30 were strongly associated with AITD. In order to determine the association of the CTLA4 gene with AITD in the Japanese, case-control association analysis for the four SNPs of the CTLA4 gene using 380 AITD patients and 266 healthy controls was done. Among the SNPs examined, the SNP JO31 was most significantly associated with AITD in the Japanese, whereas the association of the JO30 with AITD was not observed. The frequency of the disease-susceptible G allele of the JO31 of the Japanese control was higher than that of the Caucasians (67.1% vs 50.2%); however, the G allele of the JO31 was associated with Graves' disease (GD) (67.1% vs 76.3%, P=0.0013) and AITD in the Japanese (67.1% vs 74.2%, P=0.0055). Furthermore, the G allele of the JO31 was associated with the increased risk for GD [ P=0.0051, odds ratio (OR)=1.7] and AITD ( P=0.016, OR=1.5) in a dominant model. These results suggested that the CTLA4 gene is involved in the susceptibility for GD and AITD in the Japanese."
],
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[
119,
1577
]
]
}
] | [
{
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"cytotoxic T-lymphocyte antigen-4"
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215,
247
]
],
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{
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43,
48
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43,
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{
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550,
554
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],
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}
]
},
{
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],
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558,
562
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],
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]
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{
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570,
574
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{
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562
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{
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{
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},
{
"id": "77c4a217-9d3e-4b42-94d1-33397ed222a1",
"type": "variant",
"text": [
"JO31"
],
"offsets": [
[
558,
562
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "J31O"
}
]
}
] | [] | [] | [] |
46 | 15007371 | [
{
"id": "6c116e57-9a3c-4832-9595-2064f69c3e1c",
"type": "title",
"text": [
"A functional C-G polymorphism in the CYP7B1 promoter region and its different distribution in Orientals and Caucasians."
],
"offsets": [
[
0,
121
]
]
},
{
"id": "00fe5f1d-fa42-4fae-af11-77f847421698",
"type": "abstract",
"text": [
"Cytochrome P450 (CYP) 7B1 is involved in many metabolic processes including androgen metabolism. Genetic variation in the CYP7B1 gene may play a role in predisposition to prostate cancer. Here, we screened the human CYP7B1 gene for possible polymorphisms. Only one single polymorphism was detected, a C-G change in the promoter -104 base pair from the transcription start site. The allele frequency was investigated in Swedish men and compared to a Korean population, as it is known that the frequency of prostate cancer is low among Orientals. We found that the frequency of the G-allele was 4.04% in Swedes (n=150) but only 0.33% among Koreans (n=153). Computer analysis indicated that the two variants bind with different affinities to a CCAAT-box binding protein. Expression studies with reporter constructs showed significantly higher transcriptional activity of the G variant in Hek293 cells (2.7-fold, P<0.05). In conclusion, we report here for the first time the detection of a single polymorphism in the CYP7B1 gene. This polymorphism is associated with phenotypic differences in an expression system and a widely different allele frequency in two ethnic populations, with great differences in the incidence of prostate cancer."
],
"offsets": [
[
122,
1367
]
]
}
] | [
{
"id": "aed5f1bc-7377-40da-8675-385389843407",
"type": "gene",
"text": [
"Cytochrome P450 (CYP) 7B1"
],
"offsets": [
[
122,
147
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9420"
}
]
},
{
"id": "93ed21e2-52c6-4fca-af00-d094f570d1ba",
"type": "gene",
"text": [
"CYP7B1"
],
"offsets": [
[
38,
44
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9420"
}
]
},
{
"id": "c19c9b75-6132-4716-b402-d5ca2c5a9122",
"type": "gene",
"text": [
"CYP7B1"
],
"offsets": [
[
38,
44
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9420"
}
]
},
{
"id": "fff1b6a1-abb6-46c3-a876-791467ec69cc",
"type": "gene",
"text": [
"CYP7B1"
],
"offsets": [
[
38,
44
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9420"
}
]
},
{
"id": "447bc1cc-e43d-4a45-a747-5db6110a7de0",
"type": "variant",
"text": [
"C-G change in the promoter -104 base pair"
],
"offsets": [
[
429,
470
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-104G"
}
]
}
] | [] | [] | [] |
47 | 15007729 | [
{
"id": "eb0da0df-edac-4e4e-995e-f8d46c640f09",
"type": "title",
"text": [
"Fine mapping of the 2p11 dyslexia locus and exclusion of TACR1 as a candidate gene."
],
"offsets": [
[
0,
85
]
]
},
{
"id": "f72f0e84-492b-4f35-9eb5-bad0e55ef190",
"type": "abstract",
"text": [
"Developmental dyslexia, or reading disability, is a multigenic complex disease for which at least five loci, i.e. DYX1-3 and DYX5-6, have been clearly identified from the human genome. To date, DYX1C1 is the only dyslexia candidate gene cloned. We have previously reported linkage to 2p11 and 7q32 in 11 Finnish pedigrees. Here, we report the fine mapping of the approximately 40-cM linked region from chromosome 2 as we increased marker density to one per 1.8 cM. Linkage was supported with the highest NPL score of 3.0 (P=0.001) for marker D2S2216. Association analysis using the six pedigrees showing linkage pointed to marker D2S286/rs3220265 (P value <0.001) in the near vicinity of D2S2216. We went on to further characterise this approximately 15-cM candidate region (D2S2110-D2S2181) by adding six SNPs covering approximately 670 kb centred at D2S286/rs3220265 . A haplotype pattern could no longer be observed in this region, which was therefore excluded from the candidate area. This also excluded the TACR1 (tachykinin receptor 1) gene, located at marker D2S286. The dyslexia candidate region on 2p11 is, therefore, now limited to the chromosomal area D2S2116-D2S2181, which is approximately 12 Mbp of human sequence and is at a distinct location from the previously reported DYX3 locus, raising the possibility of two distinct loci on chromosome 2p."
],
"offsets": [
[
86,
1456
]
]
}
] | [
{
"id": "296ed6b2-1396-4ba7-9b86-99d08c404c83",
"type": "gene",
"text": [
"DYX1C1"
],
"offsets": [
[
281,
287
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "161582"
}
]
},
{
"id": "c155db4d-b23c-4512-b663-2a0c9e9d3710",
"type": "gene",
"text": [
"TACR1"
],
"offsets": [
[
58,
63
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6869"
}
]
},
{
"id": "b6f55756-c926-499a-93c2-1f7c8e6cc165",
"type": "gene",
"text": [
"DYX3"
],
"offsets": [
[
1381,
1385
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "11192"
}
]
},
{
"id": "08a120a9-947c-48af-b6d0-ab70585e16a1",
"type": "variant",
"text": [
"D2S286/rs3220265"
],
"offsets": [
[
719,
735
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3220265"
}
]
},
{
"id": "be4907be-6954-4cd1-b355-5ee0443a37f0",
"type": "variant",
"text": [
"D2S286/rs3220265"
],
"offsets": [
[
719,
735
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3220265"
}
]
}
] | [] | [] | [] |
48 | 15008790 | [
{
"id": "a671c667-10ec-4931-9fa2-15774e222cfe",
"type": "title",
"text": [
"Population differences in DNA sequence variation and linkage disequilibrium at the PON1 gene."
],
"offsets": [
[
0,
95
]
]
},
{
"id": "bda16d5d-992f-4a63-aeee-b87eebbd5d26",
"type": "abstract",
"text": [
"Polymorphisms of the promoter region (-108C/T) and the coding region (192Q/R) of the paraoxonase 1 gene ( PON1 ) showed differences in association with cardiovascular disease risk in various populations. To characterize the genetic variation underlying these important polymorphisms, we examined DNA sequence variation both in a 1.3-kb promoter region 16.5 kb from codon 192, and in a 1.7-kb region centered on the 192Q/R polymorphic site of the coding region of PON1 , in 30 Africans, 30 Europeans and 64 Japanese. We found 10 polymorphic sites and 11 haplotypes in the 1.3-kb promoter region and 10 biallelic polymorphic sites and 10 haplotypes in the 1.7-kb region. From the PON1 sequences of chimpanzees and an orangutan, the ancestral type of codon 192 was found to be R. The number of pairs of polymorphic sites between the promoter and 1.7-kb regions that were in significant linkage disequilibrium was much higher in a Japanese population than in African and European populations. In addition, the pairs of polymorphic sites in linkage disequilibrium differed among the three populations. These results suggest that some of the population differences in association with risk for coronary heart disease can be explained by population differences in haplotype frequency of PON1 haplotypes."
],
"offsets": [
[
96,
1403
]
]
}
] | [
{
"id": "321a2115-09f6-4755-9600-33f16acb1976",
"type": "gene",
"text": [
"paraoxonase 1 gene"
],
"offsets": [
[
186,
204
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "2754341f-812b-452e-bed8-644b650c3706",
"type": "gene",
"text": [
"PON1"
],
"offsets": [
[
84,
88
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "bd0df2a5-9d11-4b00-93d7-a4ea0a0b1553",
"type": "gene",
"text": [
"PON1"
],
"offsets": [
[
84,
88
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "9c0ffb24-f979-4385-b31d-97225ee7b055",
"type": "gene",
"text": [
"PON1"
],
"offsets": [
[
84,
88
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "4cf8c9fd-b7fd-4b4a-b2d4-f0e9d1cf545c",
"type": "gene",
"text": [
"PON1"
],
"offsets": [
[
84,
88
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "f214d583-5b3d-412e-af8c-f57df16de694",
"type": "variant",
"text": [
"(-108C/T)"
],
"offsets": [
[
134,
143
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-108T"
}
]
},
{
"id": "64ada24b-c9c0-4597-be7e-11d2a2601e0b",
"type": "variant",
"text": [
"(192Q/R)"
],
"offsets": [
[
168,
176
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "662"
}
]
}
] | [] | [] | [] |
49 | 15009068 | [
{
"id": "3e2ae00d-8b54-4b23-8da0-a9bf942eeaf0",
"type": "title",
"text": [
"Single nucleotide polymorphisms of the inflammatory cytokine genes in adults with chronic immune thrombocytopenic purpura."
],
"offsets": [
[
0,
122
]
]
},
{
"id": "601e8809-4702-408e-918a-a5dee4430dde",
"type": "abstract",
"text": [
"Single nucleotide polymorphisms (SNPs) of inflammatory cytokine genes were examined in 84 adult Japanese patients with chronic immune thrombocytopenic purpura (ITP) and 56 race-matched healthy controls. The SNPs examined were within the genes encoding tumour necrosis factor (TNF)-alpha ( -238 G/A and -308 G/A ), TNF-beta ( +252 G/A ), and interleukin (IL)-1beta ( -511 C/T and +3953 T/C ). Of these SNPs, the frequency of the TNF-beta (+252) G/G phenotype was significantly higher in ITP patients than in healthy controls (21% vs. 7%, P = 0.04, odds ratio = 3.6, 95% confidence interval 1.1-11.1), while no significant association was detected for the other SNPs. The distribution of the TNF-beta (+252) phenotype was not associated with human leucocyte antigen class II alleles or the therapeutic response in ITP patients. The frequency of circulating anti-glycoprotein IIb/IIIa antibody-producing B cells was significantly higher in ITP patients with the TNF-beta (+252) G/G phenotype than in those with the G/A or A/A phenotype (11.9 +/- 4.9 vs. 6.8 +/- 4.9 and 3.7 +/- 2.8 per 10(5) peripheral blood mononuclear cells; P = 0.02 and P < 0.001, respectively). These findings suggest that the SNP located at TNF-beta (+252) contributes to susceptibility to chronic ITP by controlling the autoreactive B-cell responses to platelet membrane glycoproteins."
],
"offsets": [
[
123,
1501
]
]
}
] | [
{
"id": "a7df69f5-f580-46f3-add9-81f965be0276",
"type": "gene",
"text": [
"tumour necrosis factor (TNF)-alpha"
],
"offsets": [
[
376,
410
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "13c0bd48-554c-4dc6-bfba-c77f521c2b77",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "f88fcc23-bdb3-411e-b5bf-a5b199c85ccf",
"type": "gene",
"text": [
"interleukin (IL)-1beta"
],
"offsets": [
[
471,
493
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3553"
}
]
},
{
"id": "0c84f3da-a5a6-480d-ba80-2d0aceeeeca9",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "65319a3b-043a-4d54-84f2-7205352131fc",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "01a009d6-ab44-4aac-9b08-928f0bacb6fb",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "7d41f194-3f15-49c7-8455-5aa2725a0311",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "d7fec9e6-22d6-4e42-aa5d-17777cd9dab1",
"type": "variant",
"text": [
"-238 G/A"
],
"offsets": [
[
414,
422
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-238A"
}
]
},
{
"id": "b0bc1fc2-3856-4d13-9f9d-cc823a58aa91",
"type": "variant",
"text": [
"-308 G/A"
],
"offsets": [
[
429,
437
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-308A"
}
]
},
{
"id": "44a74954-1256-4520-99bd-fd5382b46089",
"type": "variant",
"text": [
"+252 G/A"
],
"offsets": [
[
454,
462
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G252A"
}
]
},
{
"id": "91eb5aba-473f-4d59-97cc-3cfdf5b01a94",
"type": "variant",
"text": [
"-511 C/T"
],
"offsets": [
[
497,
505
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-511T"
}
]
},
{
"id": "96b7abaa-175d-445e-9596-ea81ad687fc2",
"type": "variant",
"text": [
"+3953 T/C"
],
"offsets": [
[
512,
521
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T3953C"
}
]
},
{
"id": "53fb615b-82d8-4273-b5bd-8b3b102012ee",
"type": "variant",
"text": [
"(+252) G/G"
],
"offsets": [
[
573,
583
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G252G"
}
]
},
{
"id": "4d6edf8f-fb01-4d74-9915-8ae7a7034b66",
"type": "variant",
"text": [
"(+252) G/G"
],
"offsets": [
[
573,
583
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G252G"
}
]
}
] | [] | [] | [] |
50 | 15022318 | [
{
"id": "e27591f3-867c-4920-a81e-2aeebdd203e2",
"type": "title",
"text": [
"Association of a programmed death 1 gene polymorphism with the development of rheumatoid arthritis, but not systemic lupus erythematosus."
],
"offsets": [
[
0,
139
]
]
},
{
"id": "241e9bbc-c433-43bc-adc6-a6aa73784f80",
"type": "abstract",
"text": [
"OBJECTIVE: The expression of autoimmunity in mice deficient in programmed death 1 ( PD-1 ) suggests that PD-1 is a candidate gene involved in the development of human autoimmune diseases such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). We therefore tested the potential association between PD-1 and the development of SLE and RA by conducting case-control genetic-association studies. METHODS: Ninety-eight SLE patients, 84 RA patients, and sex-matched control subjects for each disease group were recruited and genotyped for a single-nucleotide polymorphism, C+872T , in the human PD-1 gene. The significance of the association of the PD-1 gene with SLE or with RA was analyzed by statistical tests for the difference in genotype distribution between disease and control groups. RESULTS: The human PD-1 gene was found to be significantly associated with disease development in RA patients, but not SLE patients. The risk of RA development appeared to be significantly increased by carriage of the T allele (odds ratio 3.32, P < 0.0001) or the C/T genotype (odds ratio 3.52, P < 0.00005). CONCLUSION: The PD-1 gene is significantly associated with RA susceptibility, suggesting the possibility that PD-1 may contribute to the pathogenesis of RA."
],
"offsets": [
[
140,
1427
]
]
}
] | [
{
"id": "1d574fe0-5928-40c7-a7b9-082c2c676ca7",
"type": "gene",
"text": [
"programmed death 1"
],
"offsets": [
[
18,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "8af6de55-54e8-4db5-9f9c-ad2ff4de0068",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "987f0507-3a17-46ca-ab4d-b36bad059940",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "71f9722c-53b3-4fee-b4bd-9444f76623a9",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "cf86b358-6031-4299-8f0d-67016060a4a9",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "04348b83-bbfa-4c97-a877-591131749732",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "e659bf38-1d21-4ed6-87f4-7a4a4eb91f48",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "070e1655-7949-4a6b-a838-b6b2490cbdec",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "e7776cf7-a348-4f73-b98a-c6972d78c761",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "2d44d44d-8f15-46c4-b500-9b3b73a8f722",
"type": "variant",
"text": [
"C+872T"
],
"offsets": [
[
732,
738
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C872T"
}
]
}
] | [] | [] | [] |
51 | 15024396 | [
{
"id": "89e6cf82-e158-45db-b937-96dc3c9968a5",
"type": "title",
"text": [
"Association of the homeobox transcription factor, ENGRAILED 2 , 3, with autism spectrum disorder."
],
"offsets": [
[
0,
98
]
]
},
{
"id": "a1195aab-d093-426c-997a-f1cdbcebe38d",
"type": "abstract",
"text": [
"Mouse mutants of the homeobox transcription factor Engrailed2 (En2) and autistic individuals display similar cerebellar morphological abnormalities, which include hypoplasia and a decrease in the number of Purkinje cells. Human EN2 maps to 7q36, a chromosomal region that has demonstrated suggestive linkage to autism spectrum disorder (ASD). To investigate EN2 for evidence of association with ASD, four single-nucleotide polymorphisms (SNPs) ( rs3735653 , rs1861972 , rs1861973 , rs2361689 ) that span the majority of the 8.0 kb gene were assessed by the transmission/disequilibrium test. Initially, 138 triads of autistic individuals and their parents were tested. Two intronic SNPs ( rs1861972 and rs1861973 ) demonstrated significant association with autism ( rs1861972 , P=0.0018; rs1861973 , P=0.0003; haplotype, P=0.000005). Flanking exonic SNPs ( rs3735653 and rs2361689 ) did not display association. This analysis was then extended to include 167 small nuclear ASD pedigrees and significant association was again only observed for rs1861972 and rs1861973 under both the narrow and broad diagnostic criteria (narrow: rs1861972 P=0.0290, rs1861973 P=0.0073, haplotype P=0.0009; broad: rs1861972 P=0.0175, rs1861973 P=0.0107, haplotype P=0.0024). These data demonstrate association between a cerebellar patterning gene and ASD, suggesting a role for EN2 as a susceptibility locus and supporting a neurodevelopmental defect hypothesis in the etiology of autism."
],
"offsets": [
[
99,
1593
]
]
}
] | [
{
"id": "32aa6426-30a5-4f7b-905f-691fbfbd2d06",
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"EN2"
],
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[
328,
331
]
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"db_id": "2020"
}
]
},
{
"id": "462429db-c84e-4d82-a0ad-d5a1be4fdfc2",
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"EN2"
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328,
331
]
],
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},
{
"id": "a4dccb2f-b5a4-444e-a7ea-cdb9cba7c8bf",
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"EN2"
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]
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{
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]
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},
{
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{
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]
},
{
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575,
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],
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]
},
{
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"rs1861972"
],
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562,
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]
],
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{
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}
]
},
{
"id": "076f6e9c-805a-490b-a4ae-1ebc741dc5a6",
"type": "variant",
"text": [
"rs1861973"
],
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[
575,
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]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1861973"
}
]
}
] | [] | [] | [] |
52 | 15024686 | [
{
"id": "7e078deb-9cab-465e-92bf-bfa2e76b913f",
"type": "title",
"text": [
"Crohn disease: frequency and nature of CARD15 mutations in Ashkenazi and Sephardi/Oriental Jewish families."
],
"offsets": [
[
0,
109
]
]
},
{
"id": "323a392e-a2f5-4467-acd3-d84c5a62f47e",
"type": "abstract",
"text": [
"Crohn disease (CD), an inflammatory bowel disease, is a multifactorial trait with the highest frequency in Ashkenazi Jewish (AJ) individuals of Central European origin. Recently, three common predisposing CARD15 mutations ( R702W , G908R , and 1007fs ) and a polymorphism ( P268S ) were identified. To determine whether CARD15 mutations account for the higher prevalence of CD in AJ individuals, the haplotypes and allele frequencies of the common mutations and variants were assessed in 219 members of 50 AJ and 53 members of 10 Sephardi/Oriental Jewish (SOJ) multiplex families with CD, in 36 AJ patients with sporadic CD, and in 246 AJ and 82 SOJ controls. A higher frequency of CARD15 mutations was found in AJ patients from multiplex families with CD from Central (44.0%) versus Eastern (24.0%) Europe, especially for G908R and 1007fs , and in SOJ patients (34.5%) compared with AJ (10.1%) or SOJ (5.4%) controls. Contrary to expectation, the frequency of the common mutations was slightly lower in AJ patients with CD (30.1%) than in SOJ patients with CD (34.5%). The 702W allele was associated with both the P268 and 268S alleles. CARD15 mutation frequencies were greater in affected sib pairs than in sporadic CD cases but actually decreased in families with three or more affected sibs, raising the possibility of genetic heterogeneity. Similarly, our linkage evidence on chromosome 16 was diminished in the families with three or more affected sibs compared with sib pairs. Screening the CARD15 gene for rare variants revealed five novel changes (D113N, D357A , I363F , L550V , and N852S ) of which N852S occurred only in AJ individuals and may be disease predisposing. Also, there was no evidence for increased risk associated with the recently described IVS(+158) single-nucleotide polymorphism. Although the AJ controls appear to have a higher frequency of CARD15 mutations than the SOJ controls, it is unlikely that this difference fully explains the excess frequency of CD in the AJ population."
],
"offsets": [
[
110,
2142
]
]
}
] | [
{
"id": "eb4f924b-49c3-4384-bbf1-a540162c541a",
"type": "gene",
"text": [
"CARD15"
],
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40,
46
]
],
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]
},
{
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"CARD15"
],
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40,
46
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],
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]
},
{
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"type": "gene",
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"CARD15"
],
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[
40,
46
]
],
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}
]
},
{
"id": "5ffedbca-2db9-4d05-bf85-b81e7d1f22d4",
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"CARD15"
],
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40,
46
]
],
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]
},
{
"id": "81b8a0de-6c26-477f-9249-f2a869723569",
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"CARD15"
],
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[
40,
46
]
],
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{
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"db_id": "64127"
}
]
},
{
"id": "5457141b-6af1-43d3-b3a6-099b0c9f184e",
"type": "gene",
"text": [
"CARD15"
],
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[
40,
46
]
],
"normalized": [
{
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"db_id": "64127"
}
]
},
{
"id": "a0e2e5f0-e836-459b-bf18-62f462939965",
"type": "variant",
"text": [
"R702W"
],
"offsets": [
[
336,
341
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2066844"
}
]
},
{
"id": "daf3b1c9-fa01-44e4-b6bb-4efe4df48ebc",
"type": "variant",
"text": [
"G908R"
],
"offsets": [
[
345,
350
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2066845"
}
]
},
{
"id": "2034c9b5-3d1c-4b74-96ff-fafafc9b5712",
"type": "variant",
"text": [
"1007fs"
],
"offsets": [
[
358,
364
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5743293"
}
]
},
{
"id": "af1cdc21-8ae4-4d62-a9dd-b2369232635a",
"type": "variant",
"text": [
"P268S"
],
"offsets": [
[
388,
393
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2066842"
}
]
},
{
"id": "f6f235d4-d197-40d1-9e42-058a17d00b9d",
"type": "variant",
"text": [
"G908R"
],
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[
345,
350
]
],
"normalized": [
{
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"db_id": "2066845"
}
]
},
{
"id": "e9268b97-93d6-48db-973d-1bb99b52b5b9",
"type": "variant",
"text": [
"1007fs"
],
"offsets": [
[
358,
364
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5743293"
}
]
},
{
"id": "21a616b0-202c-44ce-89a9-b0e84e16f173",
"type": "variant",
"text": [
"D357A"
],
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[
1690,
1695
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "D357A"
}
]
},
{
"id": "4566a8ca-969c-4db9-8be1-e89853035534",
"type": "variant",
"text": [
"I363F"
],
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[
1699,
1704
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "I363F"
}
]
},
{
"id": "a71cf845-1838-4f0f-a671-6c51c4c8b82d",
"type": "variant",
"text": [
"L550V"
],
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[
1708,
1713
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "L550V"
}
]
},
{
"id": "5cc7c5d5-c2f5-4b0b-990b-29e7b16f2245",
"type": "variant",
"text": [
"N852S"
],
"offsets": [
[
1721,
1726
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "N852S"
}
]
},
{
"id": "2c169da7-8374-4e80-9db7-ba826b1c5309",
"type": "variant",
"text": [
"N852S"
],
"offsets": [
[
1721,
1726
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "N852S"
}
]
}
] | [] | [] | [] |
53 | 15026335 | [
{
"id": "490b0f71-5431-4532-9a1e-aa2ebe06301f",
"type": "title",
"text": [
"A polymorphism in the CDKN1B gene is associated with increased risk of hereditary prostate cancer."
],
"offsets": [
[
0,
100
]
]
},
{
"id": "ae9187f5-97d4-477e-b11f-4802e7001192",
"type": "abstract",
"text": [
"The loss of cell cycle control is believed to be an important mechanism in the promotion of carcinogenesis. CDKN1B (p27) belongs to the Cip/Kip family and functions as an important cell cycle gatekeeper. Several lines of evidence from clinical studies and laboratory experiments demonstrate that CDKN1B is an important tumor suppressor gene in prostate cancer etiology. In addition, a case-control study has shown that the 326T/G (V109G) polymorphism in CDKN1B is associated with advanced prostate cancer. In light of the evidence for linkage between the chromosomal location of the CDKN1B gene (12p13) and prostate cancer susceptibility in several hereditary prostate cancer (HPC) populations, we hypothesized that sequence variants of CDKN1B play a role in HPC. To test this hypothesis, we first resequenced this gene in 96 HPC probands to identify germ-line mutations and sequence variants. We then genotyped the identified sequence variants among all family members of 188 HPC families and tested for their cosegregation with prostate cancer. In total, 10 sequence variants were identified, including three nonsynonymous changes. A family-based test, which is free from the effects of population stratification, revealed a significant association between single nucleotide polymorphism (SNP) -79C/T and prostate cancer (with a nominal P of 0.0005). The C allele of -79C/T was overtransmitted from parents to their affected offspring. Evidence for this association was primarily contributed by affected offspring whose age at diagnosis was <65 years. Together with the previous association study in a sporadic prostate cancer population, our new findings additionally suggest that germ-line variants of this gene play a role in prostate cancer susceptibility."
],
"offsets": [
[
101,
1882
]
]
}
] | [
{
"id": "0f64af2d-45b7-470d-8098-03731f38896d",
"type": "gene",
"text": [
"CDKN1B"
],
"offsets": [
[
23,
29
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "1017ee5d-413d-4286-b061-8066687edfed",
"type": "gene",
"text": [
"CDKN1B"
],
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[
23,
29
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "eba844cc-8ba4-4b64-9c34-726672795596",
"type": "gene",
"text": [
"CDKN1B"
],
"offsets": [
[
23,
29
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "bf091ccc-6af9-4430-9f6d-fb569a012d2b",
"type": "gene",
"text": [
"CDKN1B"
],
"offsets": [
[
23,
29
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "7582a43d-4ae8-49bf-a5a9-e24c7a1bf4fa",
"type": "gene",
"text": [
"CDKN1B"
],
"offsets": [
[
23,
29
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "74a92b92-a82d-4490-9aef-bd295932808b",
"type": "variant",
"text": [
"326T/G"
],
"offsets": [
[
529,
536
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2066827"
}
]
},
{
"id": "dbe3dc8e-3344-421f-b72b-fbfb77923394",
"type": "variant",
"text": [
"(V109G)"
],
"offsets": [
[
539,
546
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2066827"
}
]
},
{
"id": "1f94fa11-30c2-4e06-9a62-fd4351c8fc10",
"type": "variant",
"text": [
"-79C/T"
],
"offsets": [
[
1413,
1419
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-79T"
}
]
},
{
"id": "8b9d38b2-cf38-4831-94f6-4d5c0822ca4b",
"type": "variant",
"text": [
"-79C/T"
],
"offsets": [
[
1413,
1419
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-79T"
}
]
}
] | [] | [] | [] |
54 | 15028050 | [
{
"id": "d2daf70e-0951-4e0e-906f-e0e0e99e8224",
"type": "title",
"text": [
"Additional gene variants reduce effectiveness of beta-blockers in the LQT1 form of long QT syndrome."
],
"offsets": [
[
0,
100
]
]
},
{
"id": "67330521-598e-4aa4-871b-0af0d60ad558",
"type": "abstract",
"text": [
"INTRODUCTION: Beta-blockers are widely used to prevent the lethal cardiac events associated with the long QT syndrome (LQTS), especially in KCNQ1 -related LQTS (LQT1) patients. Some LQT1 patients, however, are refractory to this therapy. METHODS AND RESULTS: Eighteen symptomatic LQTS patients (12 families) were genetically diagnosed as having heterozygous KCNQ1 variants and received beta-blocker therapy. Cardiac events recurred in 4 members (3 families) despite continued therapy during mean follow-up of 70 months. Three of these patients (2 families) had the same mutation [ A341V (KCNQ1) ]; and the other had R243H (KCNQ1) . The latter patient took aprindine, which seemed to be responsible for the event. By functional assay using a heterologous mammalian expression system, we found that A341V (KCNQ1) is a loss-of-function type mutation (not dominant negative). Further genetic screening revealed that one A341V (KCNQ1) family cosegregated with S706C (KCNH2) and another with G144S (KCNJ2) . Functional assay of the S706C (KCNH2) mutation was found to reduce the current density of expressed heterozygous KCNH2 channels with a positive shift (+8 mV) of the activation curve. Action potential simulation study was conducted based on the KYOTO model to estimate the influence of additional gene modifiers. In both models mimicking LQT1 plus 2 and LQT1 plus 7, the incidence of early afterdepolarization was increased compared with the LQT1 model under the setting of beta-adrenergic stimulation. CONCLUSION: Multiple mutations in different LQTS-related genes may modify clinical characteristics. Expanded gene survey may be required in LQT1 patients who are resistant to beta-blocker therapy."
],
"offsets": [
[
101,
1814
]
]
}
] | [
{
"id": "816e6ffe-a7f6-4d01-a903-dccc280164c0",
"type": "gene",
"text": [
"KCNQ1"
],
"offsets": [
[
242,
247
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3784"
}
]
},
{
"id": "98939c91-d0ea-4d20-a4fa-c13b459d4b4d",
"type": "gene",
"text": [
"KCNQ1"
],
"offsets": [
[
242,
247
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3784"
}
]
},
{
"id": "c58e0ec4-d27c-4297-bf42-bc90921b2e51",
"type": "variant",
"text": [
"A341V (KCNQ1)"
],
"offsets": [
[
685,
698
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "12720459"
}
]
},
{
"id": "1926a7cf-786b-4625-90a8-472408382e7e",
"type": "variant",
"text": [
"R243H (KCNQ1)"
],
"offsets": [
[
721,
734
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "R243H"
}
]
},
{
"id": "7327d5e0-d98b-4d99-9f3b-a7ea4ff0fd67",
"type": "variant",
"text": [
"A341V (KCNQ1)"
],
"offsets": [
[
685,
698
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "12720459"
}
]
},
{
"id": "54f941df-b1a5-4d94-b0ba-afca7e94cd5a",
"type": "variant",
"text": [
"A341V (KCNQ1)"
],
"offsets": [
[
685,
698
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "12720459"
}
]
},
{
"id": "c5eeba4e-4809-457e-8bf9-f48ca07a0b60",
"type": "variant",
"text": [
"S706C (KCNH2)"
],
"offsets": [
[
1065,
1078
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "S706C"
}
]
},
{
"id": "8f7a18f5-1e47-4763-976e-7ea1ad706d9d",
"type": "variant",
"text": [
"G144S (KCNJ2)"
],
"offsets": [
[
1098,
1111
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G144S"
}
]
},
{
"id": "9e1d29e7-3571-4006-8b1d-f3d91e3a67e8",
"type": "variant",
"text": [
"S706C (KCNH2)"
],
"offsets": [
[
1065,
1078
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "S706C"
}
]
}
] | [] | [] | [] |
55 | 15028669 | [
{
"id": "45304fae-7ff8-40d4-b66d-963b7123b88d",
"type": "title",
"text": [
"Polymorphisms at positions -22 and -348 in the promoter of the BAT1 gene affect transcription and the binding of nuclear factors."
],
"offsets": [
[
0,
131
]
]
},
{
"id": "57ada7a0-debc-4fd1-ab6d-7f87e98362e6",
"type": "abstract",
"text": [
"BAT1 (D6S81E, UAP56) lies in the central MHC between TNF and HLA-B , a region containing genes that affect susceptibility to immunopathologic disorders. BAT1 protein may be directly responsible for the genetic association, as antisense studies show it can down-regulate inflammatory cytokines. Here we investigate polymorphisms at positions -22 and -348 relative to the BAT1 transcription start site . DNA samples from healthy donors were used to confirm haplotypic associations with the type 1 diabetes-susceptible 8.1 ancestral haplotype (AH; HLA-A1,B8, BAT1-22*C , BAT1-348*C ,DR3) and the diabetes-resistant 7.1 AH (HLA-A3,B7, BAT1-22*C , BAT1-348*T ,DR15). Alleles carried at BAT1 -22 and -348 were in linkage disequilibrium. Electrophoretic mobility shift assays using nuclear proteins from T-cells (Jurkat and HT2), monocytes (THP1, U937) and epithelial cells (HeLa and MDA468) demonstrated DNA : protein complexes binding oligonucleotides spanning positions -22 and -348 on the 7.1 AH only. Competition assays, supershifts and molecular weight determinations suggest the complexes include the transcription factors YY1 (at -348) and Oct1 (at -22). Promoter activity was demonstrated using 520 bp and 336 bp fragments cloned from immediately upstream of the transcription start site and carrying all combinations of -22 and -348 alleles, suggesting an unidentified non-polymorphic sequence within 336 bp of the start site drives transcription. The 520 bp fragment of the BAT1 promoter cloned from the 8.1 AH was slightly less efficient than the equivalent from the 7.1 AH, whilst the reverse was observed with 336 bp fragments. This suggests BAT1 transcription on the 7.1 AH is modified by interactions involving DNA flanking positions -22 and -348."
],
"offsets": [
[
132,
1903
]
]
}
] | [
{
"id": "cafc638a-a1ff-4668-950f-b1b8cba31855",
"type": "gene",
"text": [
"BAT1"
],
"offsets": [
[
64,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7919"
}
]
},
{
"id": "14c88163-7da4-4a73-a6f5-b9500edac77d",
"type": "gene",
"text": [
"TNF"
],
"offsets": [
[
187,
190
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "44265ffb-5fa9-4785-9ea9-7303e8e03213",
"type": "gene",
"text": [
"HLA-B"
],
"offsets": [
[
197,
202
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3106"
}
]
},
{
"id": "c7ac656a-e302-4ebb-9647-bdd86f77166c",
"type": "gene",
"text": [
"BAT1"
],
"offsets": [
[
64,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7919"
}
]
},
{
"id": "6935b9c4-9fda-4407-88f4-fd67af1c735c",
"type": "gene",
"text": [
"BAT1"
],
"offsets": [
[
64,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7919"
}
]
},
{
"id": "d668ac74-82d6-4807-8f64-38252c459fdb",
"type": "gene",
"text": [
"YY1"
],
"offsets": [
[
1265,
1268
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7528"
}
]
},
{
"id": "c9cd3852-9ffc-47af-a0f7-0adb522756a7",
"type": "gene",
"text": [
"BAT1"
],
"offsets": [
[
64,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7919"
}
]
},
{
"id": "f2935268-321a-4898-9032-34fc89c04c14",
"type": "gene",
"text": [
"BAT1"
],
"offsets": [
[
64,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7919"
}
]
},
{
"id": "5c2a3831-b5f6-4f1d-9e25-5f4021351e40",
"type": "variant",
"text": [
"-22 and -348 relative to the BAT1 transcription start site"
],
"offsets": [
[
480,
538
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "5ff10d23-3f34-4f41-8e33-55bfc9d4b448",
"type": "variant",
"text": [
"BAT1-22*C"
],
"offsets": [
[
695,
704
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "22*C"
}
]
},
{
"id": "7ace9a9a-501b-4ca4-94c7-54144ba20127",
"type": "variant",
"text": [
"BAT1-348*C"
],
"offsets": [
[
707,
717
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "348*C"
}
]
},
{
"id": "86fdc601-4c5c-4eff-a6d1-561f5e063c07",
"type": "variant",
"text": [
"BAT1-22*C"
],
"offsets": [
[
695,
704
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "22C"
}
]
},
{
"id": "fcba88b1-245a-4ce6-8445-a8606a1f3e93",
"type": "variant",
"text": [
"BAT1-348*T"
],
"offsets": [
[
783,
793
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "348*T"
}
]
}
] | [] | [] | [] |
56 | 15037865 | [
{
"id": "d6246746-1400-4589-8079-9dbdf2d1a86e",
"type": "title",
"text": [
"Binge-eating episodes are not characteristic of carriers of melanocortin-4 receptor melanocortin-4 receptor gene mutations."
],
"offsets": [
[
0,
125
]
]
},
{
"id": "20a94df8-83f3-4cf5-a94d-3d8458fba23a",
"type": "abstract",
"text": [
"Recently, Branson and coworkers reported a strong association between binge-eating disorder (BED) and variants in the melanocortin-4 receptor melanocortin-4 receptor gene ( MC4R ). In the current study, we compared the eating behavior of 43 obese probands with functionally relevant MC4R mutations and of 35 polymorphism carriers ( V103I or I251L ) with wild-type carriers. The module for eating disorders of the Composite International Diagnostic Interview was used to identify binge-eating behavior. The Three-Factor Eating Questionnaire and the Leeds Food Frequency Questionnaire were used to assess restrained eating, disinhibition, hunger and percent total energy intake as fat. No significant differences between carriers of MC4R variants and wild-type carriers were detected. In particular, we found no evidence for an increased rate of binge-eating behavior in obese carriers of MC4R variants. Our findings do not support the strong association between BED and MC4R carrier status."
],
"offsets": [
[
126,
1127
]
]
}
] | [
{
"id": "ccbcdf06-2ec7-4dcf-8ebb-6ece70e9b0a3",
"type": "gene",
"text": [
"melanocortin-4 receptor"
],
"offsets": [
[
61,
84
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "afc94992-828e-48d7-98c0-f695feee806d",
"type": "gene",
"text": [
"melanocortin-4 receptor gene"
],
"offsets": [
[
85,
113
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "80f7bd3c-60ac-4bb5-bcff-af6bac1bac1c",
"type": "gene",
"text": [
"MC4R"
],
"offsets": [
[
301,
305
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "6ee56bba-2e0d-44c3-af94-175437bb5d33",
"type": "gene",
"text": [
"MC4R"
],
"offsets": [
[
301,
305
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "ab4aa65e-90c3-409b-9d32-22956ebfc8b8",
"type": "gene",
"text": [
"MC4R"
],
"offsets": [
[
301,
305
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "3c4c71e2-40e3-429a-8c37-20e0c43fa596",
"type": "gene",
"text": [
"MC4R"
],
"offsets": [
[
301,
305
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "75e90461-ca8e-4f41-8e92-61c8fb1f3ab3",
"type": "gene",
"text": [
"MC4R"
],
"offsets": [
[
301,
305
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "946b18b9-90d7-49bf-91ee-994e7e858b16",
"type": "variant",
"text": [
"V103I"
],
"offsets": [
[
462,
467
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
},
{
"id": "4dc567d0-2331-4925-ad62-47bee9c1c226",
"type": "variant",
"text": [
"I251L"
],
"offsets": [
[
473,
478
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "I251L"
}
]
}
] | [] | [] | [] |
57 | 15047633 | [
{
"id": "bd7f94c8-85c7-4de4-ad19-b2685c834070",
"type": "title",
"text": [
"Genetic variation near the hepatocyte nuclear factor-4 alpha gene predicts susceptibility to type 2 diabetes."
],
"offsets": [
[
0,
111
]
]
},
{
"id": "4cf12cad-a8fd-4b4e-9d06-6fd42422edaf",
"type": "abstract",
"text": [
"The Finland-United States Investigation Of NIDDM Genetics (FUSION) study aims to identify genetic variants that predispose to type 2 diabetes by studying affected sibling pair families from Finland. Chromosome 20 showed our strongest initial evidence for linkage. It currently has a maximum logarithm of odds (LOD) score of 2.48 at 70 cM in a set of 495 families. In this study, we searched for diabetes susceptibility variant(s) at 20q13 by genotyping single nucleotide polymorphism (SNP) markers in case and control DNA pools. Of 291 SNPs successfully typed in a 7.5-Mb interval, the strongest association confirmed by individual genotyping was with SNP rs2144908 , located 1.3 kb downstream of the primary beta-cell promoter P2 of hepatocyte nuclear factor-4 alpha ( HNF4A ). This SNP showed association with diabetes disease status (odds ratio [OR] 1.33, 95% CI 1.06-1.65, P = 0.011) and with several diabetes-related traits. Most of the evidence for linkage at 20q13 could be attributed to the families carrying the risk allele. We subsequently found nine additional associated SNPs spanning a 64-kb region, including the P2 and P1 promoters and exons 1-3. Our results and the independent observation of association of SNPs near the P2 promoter with diabetes in a separate study population of Ashkenazi Jewish origin suggests that variant(s) located near or within HNF4A increases susceptibility to type 2 diabetes."
],
"offsets": [
[
112,
1537
]
]
}
] | [
{
"id": "54a8f6cf-33e9-49f0-b263-dfc83c9e0e0b",
"type": "gene",
"text": [
"hepatocyte nuclear factor-4 alpha"
],
"offsets": [
[
28,
61
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3172"
}
]
},
{
"id": "e9dad134-2239-44d9-8c75-2d378c01c50a",
"type": "gene",
"text": [
"HNF4A"
],
"offsets": [
[
885,
890
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3172"
}
]
},
{
"id": "1f9cd85d-7098-4e48-8789-96380fd26751",
"type": "gene",
"text": [
"HNF4A"
],
"offsets": [
[
885,
890
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3172"
}
]
},
{
"id": "3c5129ce-cd4c-44f4-a30e-400d9cf772c0",
"type": "variant",
"text": [
"rs2144908"
],
"offsets": [
[
769,
778
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2144908"
}
]
}
] | [] | [] | [] |
58 | 15047636 | [
{
"id": "29b1c366-e3c6-4acf-9204-41a914591ccd",
"type": "title",
"text": [
"Association between variation in the actin-binding gene caldesmon and diabetic nephropathy in type 1 diabetes."
],
"offsets": [
[
0,
112
]
]
},
{
"id": "2726c178-67ac-4834-8225-f028b94d9cd1",
"type": "abstract",
"text": [
"Dysfunction of the actin cytoskeleton is a key event in the pathogenesis of diabetic nephropathy. We previously reported that certain cytoskeletal genes are upregulated in mesangial cells exposed to a high extracellular glucose concentration. One such gene, caldesmon , lies on chromosome 7q35, a region linked to nephropathy in family studies, making it a candidate susceptibility gene for diabetic nephropathy. We screened all exons, untranslated regions, and a 5-kb region upstream of the gene for variation using denaturing high-performance liquid chromatography technology. An A>G single nucleotide polymorphism (SNP) at position -579 in the promoter region was associated with nephropathy in a case-control study using 393 type 1 diabetic patients from Northern Ireland (odds ratio [OR] 1.38, 95% CI 1.02-1.86, P = 0.03). A similar trend was found in an independent sample from a second center. When the sample groups were combined (n = 606), the association between the -579G allele and nephropathy remained significant (OR 1.35, 1.07-1.70, P = 0.01). The haplotype structure in the surrounding 7-kb region was determined. No single haplotype was more strongly associated with nephropathy than the -579A>G SNP. These results suggest a role for the caldesmon gene in susceptibility to diabetic nephropathy in type 1 diabetes."
],
"offsets": [
[
113,
1453
]
]
}
] | [
{
"id": "317ddc58-661b-46dc-9005-cd09c70ff642",
"type": "gene",
"text": [
"caldesmon"
],
"offsets": [
[
57,
66
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "800"
}
]
},
{
"id": "29ad6e9c-2978-414d-b008-b650b4d97065",
"type": "gene",
"text": [
"caldesmon"
],
"offsets": [
[
57,
66
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "800"
}
]
},
{
"id": "e6a5ab26-525c-4647-b75f-6216f3113eb3",
"type": "variant",
"text": [
"An A>G single nucleotide polymorphism (SNP) at position -579"
],
"offsets": [
[
694,
754
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-579G"
}
]
},
{
"id": "06cb7060-36bb-4d2a-a45b-a62d6545e838",
"type": "variant",
"text": [
"-579G"
],
"offsets": [
[
1094,
1099
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-579G"
}
]
},
{
"id": "2d8d9d48-a147-4564-aae5-e86f3e22ffa1",
"type": "variant",
"text": [
"-579A>G"
],
"offsets": [
[
1324,
1331
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-579G"
}
]
}
] | [] | [] | [] |
59 | 15048652 | [
{
"id": "9692ab76-af89-4743-90fc-31da7a6a4faa",
"type": "title",
"text": [
"A novel A/G SNP in the -615th position of the dopamine D4 receptor promoter region as a source of misgenotyping of the -616 C/G SNP."
],
"offsets": [
[
0,
138
]
]
},
{
"id": "a2f3fb68-0941-4776-ac11-8bd49b2daf51",
"type": "abstract",
"text": [
"The polymorphic 5' upstream region of the dopamine D4 receptor ( DRD4 ) gene containing several single nucleotide polymorphisms (SNPs) has recently become a focus of association studies in psychiatric genetics. Most SNP genotyping methods are based on the two-step procedure of restriction fragment length polymorphism (RFLP). An alternative technique is a single-step method of allele-specific amplification (ASA), previously introduced for genotyping the -521 C/T SNP of the DRD4 promoter region and applied here for the -616 C/G SNP. Parallel genotyping of individuals with the novel ASA method and the conventionally used Ava II RFLP showed a potential underestimation of the -616 GG genotype frequency by the conventional method. Sequencing the dubious samples clearly demonstrated a novel A/G SNP at the -615th position influencing the Ava II digestion and thus resulting in misgenotyping. To avoid this problem, we introduced the Sau96 I RFLP for the -616 C/G genotyping as this restriction enzyme is not sensitive for the -615 A/G sequence variation. Allele ( -616 G = 0.48; -616 C = 0.52) and genotype ( -616 GG = 0.25; -616 GC = 0.46; -616 CC = 0.29) frequencies were determined by both the novel ASA and the Sau96 I methods. The obtained genotype frequencies corresponded to the Hardy-Weinberg equilibrium in our healthy Caucasian sample (N = 534, P = 0.168). Using these methods, no association was found between the -616 C/G SNP and personality factors of Cloninger's temperament and character inventory (N = 153) in our population."
],
"offsets": [
[
139,
1710
]
]
}
] | [
{
"id": "c47fef3b-7de5-4d54-95e4-acd7c6890af7",
"type": "gene",
"text": [
"dopamine D4 receptor"
],
"offsets": [
[
49,
69
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1815"
}
]
},
{
"id": "5619543f-d959-4409-b44a-ea9460895e01",
"type": "gene",
"text": [
"DRD4"
],
"offsets": [
[
206,
210
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1815"
}
]
},
{
"id": "5dd9bc1b-ea0c-4ad0-a52f-69db7369fdfd",
"type": "gene",
"text": [
"DRD4"
],
"offsets": [
[
206,
210
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1815"
}
]
},
{
"id": "5cb937cb-307d-406a-9ee0-fe7a5a703b03",
"type": "variant",
"text": [
"-521 C/T"
],
"offsets": [
[
599,
607
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1800955"
}
]
},
{
"id": "193d59b2-80af-4fa9-b73b-939c6d7459e4",
"type": "variant",
"text": [
"-616 C/G"
],
"offsets": [
[
124,
132
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "747302"
}
]
},
{
"id": "a725dbaf-d9bd-475b-8c21-926b7f8dde03",
"type": "variant",
"text": [
"-616 GG"
],
"offsets": [
[
828,
835
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "747302"
}
]
},
{
"id": "b1b63a87-ec34-4daa-b511-392364c4fc32",
"type": "variant",
"text": [
"A/G SNP at the -615th"
],
"offsets": [
[
945,
966
]
],
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{
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"db_id": "936462"
}
]
},
{
"id": "6b5aa63d-4559-45b4-a813-9e9252c0b03a",
"type": "variant",
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"-616 C/G"
],
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[
124,
132
]
],
"normalized": [
{
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"db_id": "747302"
}
]
},
{
"id": "d9fdb24a-c37b-4b78-a194-c8ba0c40b1c9",
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"-615 A/G"
],
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[
1184,
1192
]
],
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"db_id": "936462"
}
]
},
{
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"-616 G"
],
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828,
834
]
],
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}
]
},
{
"id": "6b36733f-825c-4604-8dd1-f6538921ecad",
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"-616 C"
],
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124,
130
]
],
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"db_id": "747302"
}
]
},
{
"id": "70e5bc88-ceea-4716-a575-47003d39d718",
"type": "variant",
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"-616 GG"
],
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828,
835
]
],
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}
]
},
{
"id": "d04f9f40-15b5-4db2-acc3-139ed967e2e1",
"type": "variant",
"text": [
"-616 GC"
],
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[
1289,
1296
]
],
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"db_id": "747302"
}
]
},
{
"id": "77092dfd-c65f-4a93-bc12-2635ff0687ab",
"type": "variant",
"text": [
"-616 CC"
],
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[
1307,
1314
]
],
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}
]
},
{
"id": "6ed4f0df-bc15-4d0b-9f3b-7b67e9656061",
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"-616 C/G"
],
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124,
132
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "747302"
}
]
}
] | [] | [] | [] |
60 | 15050452 | [
{
"id": "a3bd1ab6-ef2c-47f4-b4be-1f0ccb8c915c",
"type": "title",
"text": [
"Serum concentration and genetic polymorphism in the 5'-untraslated region of VEGF is not associated with susceptibility to HTLV-I associated myelopathy/tropical spastic paraparesis (HAM/TSP) in HTLV-I infected individuals."
],
"offsets": [
[
0,
224
]
]
},
{
"id": "600342d9-30ee-41db-80b0-3465aedaa24a",
"type": "abstract",
"text": [
"HTLV-I- associated myelopathy/tropical spastic paraparesis (HAM/TSP) is one outcome of human T-cell lymphotropic virus type I (HTLV-I) infection. It remains unknown why the majority of infected people remain healthy whereas only approximately 2-3% of infected individuals develop the disease. Recently, it has been reported that increased plasma concentrations of VEGF were significantly related to high ATL cell infiltration, and the viral transactivator Tax activates the VEGF promoter, linking the induction of angiogenesis to viral gene expression. To investigate whether VEGF promoter -634C/G single nucleotide polymorphism (SNP) and serum concentration of VEGF are associated with the development of HAM/TSP, we studied a group of 202 HAM/TSP patients, 202 asymptomatic HTLV-I seropositive carriers (HCs) and 108 seronegative healthy controls (NCs) in Kagoshima, Japan by using PCR-RFLP analysis. The serum concentration of VEGF was also compared among patients with HAM/TSP, ATL, HCs as well as with NCs. Our results indicate that both VEGF gene polymorphism and serum VEGF levels are not specifically associated with the risk of HAM/TSP in our cohort."
],
"offsets": [
[
225,
1400
]
]
}
] | [
{
"id": "c3de458e-526d-488e-85c2-5b0328085314",
"type": "gene",
"text": [
"VEGF"
],
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[
78,
82
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7422"
}
]
},
{
"id": "991ed2ba-c735-4c52-ab89-32048b92697d",
"type": "gene",
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"VEGF"
],
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78,
82
]
],
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]
},
{
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"VEGF"
],
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78,
82
]
],
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]
},
{
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"VEGF"
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78,
82
]
],
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]
},
{
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"VEGF"
],
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78,
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],
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}
]
},
{
"id": "f920e89f-93bb-4722-a238-2235ba061a6b",
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"VEGF"
],
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78,
82
]
],
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}
]
},
{
"id": "55a265cb-98b6-4e2b-be50-d0afa90cbad6",
"type": "gene",
"text": [
"VEGF"
],
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78,
82
]
],
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"db_id": "7422"
}
]
},
{
"id": "6abdea00-b411-40a8-81dd-72d995333f36",
"type": "variant",
"text": [
"-634C/G"
],
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[
822,
829
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-634G"
}
]
}
] | [] | [] | [] |
61 | 15054398 | [
{
"id": "53b894f7-572d-4147-b637-adbce0c01420",
"type": "title",
"text": [
"Candidate gene approach in association studies: would the factor V Leiden mutation have been found by this approach?"
],
"offsets": [
[
0,
118
]
]
},
{
"id": "13af86b7-96f9-4979-86ea-4b2482d04097",
"type": "abstract",
"text": [
"A re-emerging strategy in the search for disease susceptibility genes is the evaluation of candidate genes, which are thought to play a role in disease pathogenesis. Candidate genes are screened for single nucleotide polymorphisms (SNPs) in a case-control study. The factor V Leiden (FVL) mutation ( 1691G --> A in the F5 gene) is an important risk factor for venous thrombosis. We asked ourselves whether the FVL mutation would have been found using the candidate gene approach in the absence of prior knowledge of the haplotype structure of the F5 gene. We typed four SNPs in the F5 gene in the Leiden Thrombophilia study, that is, promoter ( 99930G --> A ), exon 13 ( 55907A --> G ), exon 16 ( 42855A --> G ), and intron 19 ( 37833T --> G ). These SNPs were known to have different population frequencies, making their presence in distinct haplotypes likely. None of these SNPs has previously been associated with venous thrombotic risk. Subsequently we derived haplotypes. One haplotype was clearly more frequent in patients than controls (GAAT; 20 versus 9%), suggesting that a polymorphism in or near the F5 gene in this haplotype is associated with an increased thrombotic risk. If we had sequenced the F5 gene in patients homozygous for this haplotype, in order to locate the possible causal polymorphism, we would have found that 16 (76%) patients were homozygous or heterozygous for a missense mutation in exon 10 ( 1691G --> A ), which predicts the replacement of Arg506 by Gln in one of the cleavage sites for activated protein C, a mutation that we now know as the FVL mutation ."
],
"offsets": [
[
119,
1727
]
]
}
] | [
{
"id": "a9831d83-407d-4644-b552-d2e7b4db7433",
"type": "gene",
"text": [
"F5"
],
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[
442,
444
]
],
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"db_id": "2153"
}
]
},
{
"id": "cebf8c2f-9869-4921-bac7-c1d7ab1de135",
"type": "gene",
"text": [
"F5"
],
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442,
444
]
],
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}
]
},
{
"id": "e1863aa6-345f-49a4-87a8-03098881bdf6",
"type": "gene",
"text": [
"F5"
],
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442,
444
]
],
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}
]
},
{
"id": "7e3285e0-5bc2-4bd2-9d06-ea06c06c5a5c",
"type": "gene",
"text": [
"F5"
],
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442,
444
]
],
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"db_id": "2153"
}
]
},
{
"id": "20591d31-953c-4e38-83ad-70faf69a01d2",
"type": "gene",
"text": [
"F5"
],
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[
442,
444
]
],
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"db_name": "NCBI Gene",
"db_id": "2153"
}
]
},
{
"id": "54a88ff7-0b3e-40e8-bc65-8fd841786236",
"type": "variant",
"text": [
"factor V Leiden (FVL) mutation"
],
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[
387,
417
]
],
"normalized": [
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"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "68b109af-f22c-4c43-a105-5cad706e0741",
"type": "variant",
"text": [
"1691G --> A"
],
"offsets": [
[
421,
432
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G1691A"
}
]
},
{
"id": "d0f72090-21e0-4798-b6a3-11a8d011ed0a",
"type": "variant",
"text": [
"99930G --> A"
],
"offsets": [
[
773,
785
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G99930A"
}
]
},
{
"id": "e61fad8a-c6f4-4e0b-b2f3-3bc36af4324d",
"type": "variant",
"text": [
"55907A --> G"
],
"offsets": [
[
799,
811
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A55907G"
}
]
},
{
"id": "c9af97df-8913-4ed9-94c2-898b0be2943c",
"type": "variant",
"text": [
"42855A --> G"
],
"offsets": [
[
825,
837
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A42855G"
}
]
},
{
"id": "6e0ce533-b887-4806-8b95-df55f9745238",
"type": "variant",
"text": [
"37833T --> G"
],
"offsets": [
[
857,
869
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T37833G"
}
]
},
{
"id": "aaac7dea-0341-41f1-b0f9-0af4736b2543",
"type": "variant",
"text": [
"1691G --> A"
],
"offsets": [
[
421,
432
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G1691A"
}
]
},
{
"id": "f3914e94-ccda-4bbb-ad4e-7ba177be9c67",
"type": "variant",
"text": [
"Arg506 by Gln"
],
"offsets": [
[
1608,
1621
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "R506Q"
}
]
},
{
"id": "5b03137f-567d-4d52-b339-1c68cbfefe42",
"type": "variant",
"text": [
"FVL mutation"
],
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[
534,
546
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
}
] | [] | [] | [] |
62 | 15057901 | [
{
"id": "f373dd4d-4677-469c-86e6-f7d049014533",
"type": "title",
"text": [
"Variation of hepatic glucuronidation: Novel functional polymorphisms of the UDP-glucuronosyltransferase UGT1A4 ."
],
"offsets": [
[
0,
113
]
]
},
{
"id": "27b1f880-962b-4b38-9ad0-f1548c04181e",
"type": "abstract",
"text": [
"UDP-glucuronosyltransferases are a family of drug metabolizing enzymes contributing to hepatic drug metabolism and protection against environmental toxins. The aim of this study was to identify polymorphisms at the human UGT1A gene locus and to characterize their function and potential association with hepatocellular carcinoma (HCC). Genomic DNA from the blood of 363 subjects (128 patients with HCC, 235 blood donors) was analyzed for polymorphisms of the UGT1A3 , UGT1A4 , UGT1A8 , UGT1A9 , UGT1A1 , UGT1A10 genes using polymerase chain reaction, sequencing analysis. Recombinant variant UGT protein was analyzed by activity assays. In the UGT1A8 gene an A173G variant and a conserved G to A exchange at position 765 were detected in 25% and 15%. UGT1A9 exhibited two variants C3Y and M33T in 1% and 3%. UGT1A1 , UGT1A10 exhibited conserved nucleotide exchanges ( 128 G-->A and 696 C-->T ) in 2% and 13%. In the UGT1A3 gene a W11R , a V47A variant, and a conserved G to A exchange at position 81 with an incidence of 65%, 58%, and 65%, respectively, were identified. UGT1A4 exhibited a P24T and an L48V variant in 8% and 9%. UGT1A SNPs were not associated with HCC. UGT1A4 P24T and L48V exhibited reduced glucuronidation activities: beta-naphthylamine 30% and 50%, and dihydrotestosterone 50% and 0%, respectively. In conclusion, the high prevalence of SNPs throughout the human UGT1A gene locus illustrates a genetic basis of interindividual variations of hepatic metabolism. Two polymorphisms of the hepatic UGT1A4 protein show a differential metabolic activity toward mutagenic amines and endogenous steroids, altering hepatic metabolism and detoxification."
],
"offsets": [
[
114,
1823
]
]
}
] | [
{
"id": "36957aef-43e4-4668-a944-7b7068303abb",
"type": "gene",
"text": [
"UGT1A3"
],
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[
574,
580
]
],
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"db_id": "54659"
}
]
},
{
"id": "fda23a1b-eb48-4008-83e8-ba0f1a4bbf3e",
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105,
111
]
],
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]
},
{
"id": "ee4e892f-7831-40f6-935b-7fe53c0030e9",
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"UGT1A8"
],
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594,
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]
],
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]
},
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604,
610
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]
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{
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614,
620
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],
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]
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{
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624,
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]
},
{
"id": "3eba0530-5d81-4bc0-bbe9-250050968227",
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594,
600
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],
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},
{
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604,
611
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],
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]
},
{
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614,
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],
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]
},
{
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624,
631
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],
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},
{
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574,
580
]
],
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]
},
{
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"UGT1A4"
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105,
111
]
],
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]
},
{
"id": "737325ce-0349-49a1-9529-d3a97c173ddb",
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"UGT1A4"
],
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105,
111
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],
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]
},
{
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105,
111
]
],
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"db_id": "54657"
}
]
},
{
"id": "af435e46-b364-4f69-acea-18190ed57362",
"type": "variant",
"text": [
"A173G"
],
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[
783,
788
]
],
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"db_id": "A173G"
}
]
},
{
"id": "cba51602-137e-4d10-a68b-66bd3ae4d578",
"type": "variant",
"text": [
"G to A exchange at position 765"
],
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815,
846
]
],
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"db_id": "G765A"
}
]
},
{
"id": "a92da035-088b-48f4-9059-b4e0880cf61b",
"type": "variant",
"text": [
"C3Y"
],
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[
911,
914
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C3Y"
}
]
},
{
"id": "c8fa901b-944a-4fac-b0d1-cb96adc55bf0",
"type": "variant",
"text": [
"M33T"
],
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[
921,
925
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "M33T"
}
]
},
{
"id": "5f2e3f62-a15d-4294-9ffc-11147c39dbe6",
"type": "variant",
"text": [
"128 G-->A"
],
"offsets": [
[
1004,
1013
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G128A"
}
]
},
{
"id": "4686ac76-ec79-4716-aa5a-e71c00c8a1e3",
"type": "variant",
"text": [
"696 C-->T"
],
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[
1020,
1029
]
],
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"db_name": "HGVS-like",
"db_id": "C696T"
}
]
},
{
"id": "d93e8098-4ea5-4d01-90fb-f1433b743e37",
"type": "variant",
"text": [
"W11R"
],
"offsets": [
[
1071,
1075
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "W11R"
}
]
},
{
"id": "996d6eb6-328f-4d86-8e76-433683b52bc5",
"type": "variant",
"text": [
"V47A"
],
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1081,
1085
]
],
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"db_name": "HGVS-like",
"db_id": "V47A"
}
]
},
{
"id": "de0d8830-7215-4e24-ab4c-af9708976b64",
"type": "variant",
"text": [
"G to A exchange at position 81"
],
"offsets": [
[
1113,
1143
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G81A"
}
]
},
{
"id": "c2ecce8e-63e5-4e1b-8597-5cfe4caa004d",
"type": "variant",
"text": [
"P24T"
],
"offsets": [
[
1238,
1242
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "P24T"
}
]
},
{
"id": "1c4745f6-de8c-415e-8216-a65c9043ef07",
"type": "variant",
"text": [
"L48V"
],
"offsets": [
[
1252,
1256
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "L48V"
}
]
},
{
"id": "52a013fa-5c76-41d1-9bea-2aec469c1449",
"type": "variant",
"text": [
"P24T"
],
"offsets": [
[
1238,
1242
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "P24T"
}
]
},
{
"id": "bca0373e-aedd-4433-8b70-965f92ec4f3c",
"type": "variant",
"text": [
"L48V"
],
"offsets": [
[
1252,
1256
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "L48V"
}
]
}
] | [] | [] | [] |
63 | 15061869 | [
{
"id": "837e4a63-1327-4c49-83d5-eb27f943dfb0",
"type": "title",
"text": [
"A single-nucleotide polymorphism in the human p27kip1 gene ( -838C>A ) affects basal promoter activity and the risk of myocardial infarction."
],
"offsets": [
[
0,
143
]
]
},
{
"id": "222452ac-9d30-491d-8c3d-fa94695ad488",
"type": "abstract",
"text": [
"BACKGROUND: Excessive proliferation of vascular smooth muscle cells and leukocytes within the artery wall is a major event in the development of atherosclerosis. The growth suppressor p27kip1 associates with several cyclin-dependent kinase/cyclin complexes, thereby abrogating their capacity to induce progression through the cell cycle. Recent studies have implicated p27kip1 in the control of neointimal hyperplasia. For instance, p27kip1 ablation in apolipoprotein-E-null mice enhanced arterial cell proliferation and accelerated atherogenesis induced by dietary cholesterol. Therefore, p27kip1 is a candidate gene to modify the risk of developing atherosclerosis and associated ischaemic events (i.e., myocardial infarction and stroke). RESULTS: In this study we found three common single-nucleotide polymorphisms in the human p27kip1 gene ( +326T>G [V109G] , -79C>T , and -838C>A ). The frequency of -838A carriers was significantly increased in myocardial infarction patients compared to healthy controls (odds ratio [OR] = 1.73, 95% confidence interval [95%CI] = 1.12-2.70). In addition, luciferase reporter constructs driven by the human p27kip1 gene promoter containing A at position -838 had decreased basal transcriptional activity when transiently transfected in Jurkat cells, compared with constructs bearing C in -838 (P = 0.04). CONCLUSIONS: These data suggest that -838A is associated with reduced p27kip1 promoter activity and increased risk of myocardial infarction."
],
"offsets": [
[
144,
1652
]
]
}
] | [
{
"id": "d5f786d9-b4aa-4dd4-ba29-157277e527ae",
"type": "gene",
"text": [
"p27kip1"
],
"offsets": [
[
47,
54
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "5269e4ed-30b4-4a3c-8620-bdd71fc36ea0",
"type": "gene",
"text": [
"p27kip1"
],
"offsets": [
[
47,
54
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "80a01f02-1b65-4378-b973-09716dc1ce46",
"type": "gene",
"text": [
"p27kip1"
],
"offsets": [
[
47,
54
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "cad09a5e-fa2a-4db8-8f6d-76319a30ba97",
"type": "gene",
"text": [
"p27kip1"
],
"offsets": [
[
47,
54
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "4540de13-45de-4f01-a992-89cc55d45c22",
"type": "gene",
"text": [
"p27kip1"
],
"offsets": [
[
47,
54
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "fbb03430-fa92-4e61-a386-e1e6d3c08b3d",
"type": "gene",
"text": [
"p27kip1"
],
"offsets": [
[
47,
54
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "76981a85-7562-4464-8b65-213e0dbe3e69",
"type": "gene",
"text": [
"p27kip1"
],
"offsets": [
[
47,
54
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1027"
}
]
},
{
"id": "a5ba55fd-c44c-4430-92e7-6c97e1dbc8de",
"type": "variant",
"text": [
"+326T>G [V109G]"
],
"offsets": [
[
1000,
1015
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2066827"
}
]
},
{
"id": "3cb99680-3583-4610-b179-a32bbe04519b",
"type": "variant",
"text": [
"-79C>T"
],
"offsets": [
[
1019,
1025
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-79T"
}
]
},
{
"id": "1f98e351-88d7-403c-a858-16b996a9953a",
"type": "variant",
"text": [
"-838C>A"
],
"offsets": [
[
63,
70
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-838A"
}
]
},
{
"id": "7dbb6c6e-e1b8-44cb-9886-c362c156e7f4",
"type": "variant",
"text": [
"-838A"
],
"offsets": [
[
1062,
1067
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-838A"
}
]
},
{
"id": "4b90e02e-a84a-4bcf-99cb-4b504cf39228",
"type": "variant",
"text": [
"A at position -838"
],
"offsets": [
[
1340,
1358
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-838A"
}
]
},
{
"id": "352338b6-8315-44de-8ea4-76eaee227b4e",
"type": "variant",
"text": [
"C in -838"
],
"offsets": [
[
1485,
1494
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-838C"
}
]
},
{
"id": "271ca3a8-e1b8-4528-b696-f5f7a3b2379f",
"type": "variant",
"text": [
"-838A"
],
"offsets": [
[
1062,
1067
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-838A"
}
]
}
] | [] | [] | [] |
64 | 15066320 | [
{
"id": "8bf968b0-879a-47a1-8fe5-9a9e447bd696",
"type": "title",
"text": [
"Chromosome 11 monosomy in conjunction with a mutated SDHD initiation codon in nonfamilial paraganglioma cases."
],
"offsets": [
[
0,
112
]
]
},
{
"id": "de6821a0-8031-41ff-9a5e-9df9924f01fd",
"type": "abstract",
"text": [
"Paragangliomas of the head and neck region are a group of rare, usually benign, slow-growing tumors developing from paraganglionic chemoreceptors in most patients. Mutations in a subunit of the mitochondrial enzyme II complex (succinate dehydrogenase [SDHD]) were shown to be responsible for the formation of paragangliomas. In addition, loss of heterozygosity (LOH) on chromosome 11, mainly in 11q23 ( PGL1 ), was observed recently. We analyzed DNA derived from tumor sections of three unrelated paraganglioma patients (one case with multiple paragangliomas, two cases with single tumors; all of them sporadic cases) for mutations in the SDHD gene by direct sequencing. Microsatellite-based LOH was performed, and events of chromosomal loss were validated by fluorescence in situ hybridization (FISH) on paraffin-embedded tumor and normal tissue by using centromeric satellite DNA. Sequence analysis revealed mutations in SDHD exon 1 in all patients, affecting the initiation codon ( M1V ). Another alteration was detected in exon 2 but was lacking in tumor DNA and therefore classified as polymorphism ( H50R ). LOH and FISH analyses demonstrated partial/total monosomy for chromosome 11 in the tumor samples tested. A common genetic mechanism appears to be the pathophysiologic basis for sporadic tumor development because the proposed two-hit model comprising both LOH and point mutation is manifest in our patients. Loss of chromosome 11 regions, including the deletion of PGL1 and PGL2 loci, may result in a more severe phenotype, as exemplified by the development of multiple tumors in one of the patients."
],
"offsets": [
[
113,
1736
]
]
}
] | [
{
"id": "e0ab0543-0e2e-4d0e-b2b6-3b4f4f6b8eae",
"type": "gene",
"text": [
"mitochondrial enzyme II complex (succinate dehydrogenase [SDHD])"
],
"offsets": [
[
308,
372
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6392"
}
]
},
{
"id": "6f0576bb-bac2-4bb6-a1f9-9a658c7fff89",
"type": "gene",
"text": [
"PGL1"
],
"offsets": [
[
518,
522
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6392"
}
]
},
{
"id": "f0d3c0d0-63a5-48c0-9229-74e3df8aaa9b",
"type": "gene",
"text": [
"SDHD"
],
"offsets": [
[
54,
58
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6392"
}
]
},
{
"id": "5c144cb9-3d3d-4673-be8e-0a04b627dd89",
"type": "gene",
"text": [
"SDHD"
],
"offsets": [
[
54,
58
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6392"
}
]
},
{
"id": "9e788d2b-21c7-442e-b042-0926c7a69642",
"type": "gene",
"text": [
"PGL1"
],
"offsets": [
[
518,
522
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6392"
}
]
},
{
"id": "6736d6ce-64be-475d-9e1e-c857069125ce",
"type": "gene",
"text": [
"PGL2"
],
"offsets": [
[
1609,
1613
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5235"
}
]
},
{
"id": "413260b4-a055-4fb1-be52-0e13452db405",
"type": "variant",
"text": [
"M1V"
],
"offsets": [
[
1104,
1107
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "M1V"
}
]
},
{
"id": "931a4dca-220d-496c-aae4-135e43506cb7",
"type": "variant",
"text": [
"H50R"
],
"offsets": [
[
1225,
1229
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "11214077"
}
]
}
] | [] | [] | [] |
65 | 15077293 | [
{
"id": "035432b5-886e-4dfd-b916-c5992f1ab4b0",
"type": "title",
"text": [
"A functional haplotype of the PADI4 gene associated with rheumatoid arthritis in a Japanese population is not associated in a United Kingdom population."
],
"offsets": [
[
0,
154
]
]
},
{
"id": "44c323eb-30b0-4bae-9f1b-a36f6f0b2300",
"type": "abstract",
"text": [
"OBJECTIVE: In the era of postgenomic research, linkage- and association-based strategies are beginning to reveal novel complex disease genes. Using such an approach, a functional haplotype of the peptidylarginine deiminase 4 gene ( PADI4 ) has recently been identified as a gene conferring susceptibility to rheumatoid arthritis (RA) in a Japanese population. In the present study, we investigated the association of single-nucleotide polymorphisms (SNPs) in the PADI4 gene with RA in a UK population. METHODS: Association with 4 exonic SNPs ( padi4_89*G/A , padi4_90*T/C , padi4_92*G/C , and padi4_104*T/C ), mapping to the PADI4 gene and defining a haplotype previously reported to be associated with RA, was investigated. Genotyping was performed using 5' allelic discrimination assays. Estimated haplotypes were generated using the expectation-maximization algorithm, and frequencies of the SNPs and haplotypes were compared between unrelated Caucasian RA patients from the UK (n = 839) and population controls (n = 481). RESULTS: Allele frequencies for the 4 SNPs in the UK population were similar to those reported in the Japanese control population, but none of these was associated with RA. As in the Japanese population, the SNPs in the UK population defined 2 major haplotypes, but neither was associated with RA (P = 0.79). CONCLUSION: A PADI4 susceptibility haplotype associated with RA in a Japanese population is not associated with RA in a UK population. Other genes involved in the citrullinating pathway remain strong candidate RA-susceptibility genes and require further investigation."
],
"offsets": [
[
155,
1769
]
]
}
] | [
{
"id": "29e908e8-2054-4ee6-84d6-614ef1d4231d",
"type": "gene",
"text": [
"peptidylarginine deiminase 4 gene"
],
"offsets": [
[
352,
385
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "23569"
}
]
},
{
"id": "c6530991-b463-4b09-bce7-a72b8641c4f9",
"type": "gene",
"text": [
"PADI4"
],
"offsets": [
[
31,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "23569"
}
]
},
{
"id": "936a3ff4-3438-4c28-a94d-6bab8554073b",
"type": "gene",
"text": [
"PADI4"
],
"offsets": [
[
31,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "23569"
}
]
},
{
"id": "15d2a0c2-5f23-4973-9644-e79670043174",
"type": "gene",
"text": [
"PADI4"
],
"offsets": [
[
31,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "23569"
}
]
},
{
"id": "6696d1f2-36d6-4762-aefd-566785e279ed",
"type": "gene",
"text": [
"PADI4"
],
"offsets": [
[
31,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "23569"
}
]
},
{
"id": "7082463c-ecc5-4457-ab66-348f0a4b14da",
"type": "variant",
"text": [
"padi4_89*G/A"
],
"offsets": [
[
703,
715
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G89*A"
}
]
},
{
"id": "e23d678b-3168-47d7-bef6-116162d301c4",
"type": "variant",
"text": [
"padi4_90*T/C"
],
"offsets": [
[
719,
731
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T90*C"
}
]
},
{
"id": "df511605-1875-4e8e-96c8-bd9accdb57fa",
"type": "variant",
"text": [
"padi4_92*G/C"
],
"offsets": [
[
735,
747
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G92*C"
}
]
},
{
"id": "12691e41-e656-4d5c-9ab2-05ea3c0bb22b",
"type": "variant",
"text": [
"padi4_104*T/C"
],
"offsets": [
[
755,
768
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T104*C"
}
]
}
] | [] | [] | [] |
66 | 15078863 | [
{
"id": "7500a789-7f10-448f-bd79-03a9d21635a2",
"type": "title",
"text": [
"C242T CYBA polymorphism of the NADPH oxidase is associated with reduced respiratory burst in human neutrophils."
],
"offsets": [
[
0,
114
]
]
},
{
"id": "74a645a7-e0c4-474a-bc75-db8f7521c116",
"type": "abstract",
"text": [
"Oxidative stress contributes to the pathogenesis of atherosclerosis. p22phox-based NAD(P)H oxidases exist in the vessel wall, acting as important superoxide-generating systems in the vasculature. Some studies have identified reduced atherosclerosis in the presence of the C242T CYBA polymorphism, whereas others have not. Because vascular p22phox is identical to neutrophil p22phox , we studied the association between the C242T , A640G , and -930A/G CYBA polymorphisms and the quantity of superoxide produced from neutrophils isolated from healthy adults to determine if these polymorphisms had any functional impact on NADPH oxidase function. Neutrophils were isolated from 90 subjects by Percoll density gradient centrifugation. Genotypes were determined by polymerase chain reaction (PCR) and restriction mapping, as well as real-time PCR. The oxidative burst was stimulated with phorbol 12-myristate 13-acetate. Superoxide was quantified using the superoxide dismutase inhibitable oxidation of the spin probe hydroxylamine 1-hydroxy-3-carboxy-pyrrolidine, detected by electron paramagnetic resonance. Superoxide production was significantly affected by the C242T polymorphism, being 8.7+/-0.7, 7.9+/-0.6, and 5.9+/-1.2 micromol/L per minute per 10(6) neutrophils for the C242T CC, CT, and TT genotypes, respectively (P<0.05). In contrast, the A640G and the -930A/G polymorphisms did not alter the neutrophil respiratory burst. Phagocytic respiratory burst activity in homozygous individuals with the T allele of the C242T CYBA polymorphism is significantly lower than of wild-type carriers and heterozygous individuals. Because p22phox exists in both the neutrophil and vessel wall, vascular oxidative stress is likely diminished in individuals with this polymorphism."
],
"offsets": [
[
115,
1921
]
]
}
] | [
{
"id": "62e12713-439f-4941-a5d9-b209990b0b14",
"type": "gene",
"text": [
"p22phox-based NAD(P)H oxidases"
],
"offsets": [
[
185,
215
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "9ea2c3e7-05ad-44bb-92a8-b2c44b8e9f3f",
"type": "gene",
"text": [
"CYBA"
],
"offsets": [
[
6,
10
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "35fb19c8-0186-492e-9fe9-de5d43c472f4",
"type": "gene",
"text": [
"p22phox"
],
"offsets": [
[
185,
192
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "a81c2571-2c23-4e4d-88e5-20bbf0762bad",
"type": "gene",
"text": [
"p22phox"
],
"offsets": [
[
185,
192
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "d07a55a3-4233-4127-beca-7cd6a2bf91ff",
"type": "gene",
"text": [
"CYBA"
],
"offsets": [
[
6,
10
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "16810fb3-88c1-4d33-8ab7-656f4ee9fc3a",
"type": "gene",
"text": [
"NADPH oxidase"
],
"offsets": [
[
33,
46
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "4a3dcdb9-53bf-4b43-bcbe-d4e8473f608c",
"type": "gene",
"text": [
"superoxide dismutase"
],
"offsets": [
[
1086,
1106
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6647"
}
]
},
{
"id": "54dd1dac-ed8d-412e-a49f-1c7c2a923a67",
"type": "gene",
"text": [
"CYBA"
],
"offsets": [
[
6,
10
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "232424a1-ad22-4aca-aae5-0bb0b8c8cf40",
"type": "gene",
"text": [
"p22phox"
],
"offsets": [
[
185,
192
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "fc2fde35-bb5f-45f6-b0cc-61e4ac2c655d",
"type": "variant",
"text": [
"C242T"
],
"offsets": [
[
0,
5
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C242T"
}
]
},
{
"id": "e87f4f3f-a753-42e2-8e7b-c0bda4be20a3",
"type": "variant",
"text": [
"C242T"
],
"offsets": [
[
0,
5
]
],
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}
]
},
{
"id": "2b6f6af9-b88f-458b-b8ef-a89bb48d1a2a",
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"A640G"
],
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557,
562
]
],
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{
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}
]
},
{
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"-930A/G"
],
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570,
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]
],
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{
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"db_id": "A-930G"
}
]
},
{
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{
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{
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{
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{
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}
]
}
] | [] | [] | [] |
67 | 15080568 | [
{
"id": "77407811-6807-4e23-a9c4-93702aa2442b",
"type": "title",
"text": [
"The glutathione S-transferase polymorphisms in a control population and in Alzheimer's disease patients."
],
"offsets": [
[
0,
106
]
]
},
{
"id": "c22fe894-2896-4a89-8717-df465dad956c",
"type": "abstract",
"text": [
"In this study, we investigated the role of glutathione S-transferase P1 ( GSTP1 ) polymorphisms in the pathogenesis of Alzheimer's disease (AD). We genotyped the GSTP1 polymorphisms in exon 5 ( A313G ) and exon 6 ( C341T ) by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 56 Croatian patients with AD and 231 controls. Distributions and frequencies of GSTP1 genetic variants were not statistically different between AD patients and healthy controls. Higher frequencies of the mutant genotypes were observed in AD patients (13% for both A313G and C341T ) when compared with control subjects (7% for A313G and 8% for C341T ), but association of GSTP1 GG (OR 2.057, 95% CI 0.796-5.315, p=0.094) and TT (OR 1.691, 95% CI 0.669-4.270, p=0.514) genotypes with an increased risk of AD was not confirmed by statistical analysis. The frequencies of GSTP1 alleles (A, B, C, D) did not significantly differ between AD patients and controls and they were indicated as follows: 52.7%, 15.2%, 12.5% and 19.6% for AD cases and 58.4%, 14.1%, 14.1% and 13.4% for controls. The estimation of the GSTP1 haplotype distribution showed that GSTP1*A/GSTP1*B and GSTP1*A/GSTP1*C haplotypes were less frequent, while GSTP1*B/GSTP1*B and GSTP1*C/GSTP1*D haplotypes were more frequent in AD patients than in controls. In conclusion, the involvement of GSTP1 alleles in individual susceptibility to AD was not confirmed as statistically significant in the tested Croatian Caucasian population. A possible role of GSTP1 in the complex etiopathogenesis of AD is further discussed, based on observed differences in haplotype distribution and higher frequencies of mutant genotypes in AD patients."
],
"offsets": [
[
107,
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]
]
}
] | [
{
"id": "93b98da1-ddc0-414e-aa91-854dc9dc4759",
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"glutathione S-transferase P1"
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151,
179
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],
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]
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{
"id": "9d23403d-c16c-47b5-ac16-a00291fd36c5",
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"GSTP1"
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183,
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{
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{
"id": "c97b77c9-5789-4cb6-bdb5-4c6761a65360",
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"GSTP1"
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183,
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},
{
"id": "b7ab6b5e-8f39-42c3-a971-4ef24a413b8b",
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"GSTP1"
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183,
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],
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]
},
{
"id": "138d1bb5-1d24-4ba0-8594-fa27e615ec25",
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"GSTP1"
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183,
188
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],
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]
},
{
"id": "a9287800-f83a-4c37-a936-f53d093a8efe",
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"GSTP1"
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183,
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],
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]
},
{
"id": "b53fbe26-ac3c-4994-be6e-2bc402a56731",
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"GSTP1"
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183,
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],
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]
},
{
"id": "16657d84-156d-4611-be26-b58b89329239",
"type": "variant",
"text": [
"A313G"
],
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305,
310
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],
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]
},
{
"id": "6a3b3161-03f7-428b-99b2-b593661ebff8",
"type": "variant",
"text": [
"C341T"
],
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326,
331
]
],
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{
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}
]
},
{
"id": "eaf62c0b-2e61-46ab-b8df-c417dfb7c72c",
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"A313G"
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305,
310
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],
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}
]
},
{
"id": "20981590-b21f-461f-bfa3-27ead4174326",
"type": "variant",
"text": [
"C341T"
],
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326,
331
]
],
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"db_id": "1138272"
}
]
},
{
"id": "7acf4349-869b-45ad-b364-da4319b69f8f",
"type": "variant",
"text": [
"A313G"
],
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305,
310
]
],
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}
]
},
{
"id": "4f851653-546c-4d4c-8481-911c9103bd71",
"type": "variant",
"text": [
"C341T"
],
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326,
331
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],
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}
]
},
{
"id": "917708d0-ca86-429a-8a68-25260dddaf7d",
"type": "variant",
"text": [
"GSTP1*A/GSTP1*B"
],
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[
1280,
1295
]
],
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{
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"db_id": "null"
}
]
},
{
"id": "fb70aad1-f96b-4ce1-ad99-71d9991c0566",
"type": "variant",
"text": [
"GSTP1*A/GSTP1*C"
],
"offsets": [
[
1302,
1317
]
],
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{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "a89e9b0c-6c8b-40e4-b92a-da438ea81aa3",
"type": "variant",
"text": [
"GSTP1*B/GSTP1*B"
],
"offsets": [
[
1357,
1372
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "e76f810b-40b9-40ff-b9e2-9cd879cf50cd",
"type": "variant",
"text": [
"GSTP1*C/GSTP1*D"
],
"offsets": [
[
1379,
1394
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
}
] | [] | [] | [] |
68 | 15084241 | [
{
"id": "1e02335b-f33b-4498-81ca-da4c4d240b8a",
"type": "title",
"text": [
"Estrogen receptor-alpha polymorphism in a Taiwanese clinical breast cancer population: a case-control study."
],
"offsets": [
[
0,
109
]
]
},
{
"id": "dde6bc6c-b35e-4f2c-8c7a-2fe37880b9c2",
"type": "abstract",
"text": [
"INTRODUCTION: Receptor-mediated estrogen activation participates in the development and progression of breast cancer. Estrogen receptor (ER)-alpha polymorphism has been found to be associated with breast cancer and clinical features of the disease in Caucasians. Epidemiologic studies have revealed that age-incidence patterns of breast cancer in Asians differ from those in Caucasians. Genomic data for ER-alpha in either population is therefore of value in the clinical setting for that ethnic group. METHODS: A case-control study was conducted to establish a database of ER-alpha polymorphisms in a Taiwanese population in order to compare Western and Taiwanese (Asian) distributions and to evaluate ER-alpha polymorphism as an indicator of clinical outcome. The ER-alpha gene was scanned in a Taiwanese clinical breast cancer group (189 patients) and in healthy individuals (177 healthy control individuals). PCR single-strand conformation polymorphism technology was employed and real-time PCR melting curve analysis was performed. RESULTS: Three sites of silent single nucleotide polymorphism (SNPs) were found, as reported previously in Western studies, but at significantly different frequencies. Among the three SNPs, the frequency of allele 1 (TCT --> TCC) in codon 10 was significantly lower in breast cancer patients (32.0%) than in control individuals (40.4%; P = 0.018). We found that allele 1 (ACG --> ACA) in codon 594 was less common in breast cancer patients with a family history of breast cancer (5.9%) than in those without such a history (19.6%; P = 0.049). Individually, both allele 1 in codon 325 (CCC --> CCG) and allele 1 in codon 594 exhibited a reverse association with the occurrence of lymph node metastasis. Furthermore, incorporation of both SNP markers further increased predictive accuracy. CONCLUSIONS: Our data suggest that ER-alpha polymorphisms are correlated with various aspects of breast cancer in Taiwan. ER-alpha genotype, as determined during presurgical evaluation, might represent a surrogate marker for predicting breast cancer lymph node metastasis."
],
"offsets": [
[
110,
2229
]
]
}
] | [
{
"id": "7e85f59b-d8e3-4431-91da-3fb1f30eac8a",
"type": "gene",
"text": [
"Estrogen receptor (ER)-alpha"
],
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229,
257
]
],
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]
},
{
"id": "3a50b4cb-06ec-4a3d-8666-3685f8d29d58",
"type": "gene",
"text": [
"ER-alpha"
],
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517,
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]
],
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]
},
{
"id": "aed9fc9c-4a83-4e0d-8cbb-ea81e49a607c",
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"ER-alpha"
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517,
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]
},
{
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"ER-alpha"
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517,
525
]
],
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}
]
},
{
"id": "feec2fe5-da23-4033-95ab-173b5dd115d5",
"type": "gene",
"text": [
"ER-alpha"
],
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517,
525
]
],
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"db_id": "2099"
}
]
},
{
"id": "775b472c-728f-4f3e-86bd-03f42952ce1d",
"type": "gene",
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"ER-alpha"
],
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[
517,
525
]
],
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}
]
},
{
"id": "77c03a5f-7eec-4312-b0c8-97fb40821bb2",
"type": "gene",
"text": [
"ER-alpha"
],
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[
517,
525
]
],
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}
]
},
{
"id": "c0c9e560-9f50-4f24-80a8-b136b3c0a7c0",
"type": "variant",
"text": [
"(TCT --> TCC) in codon 10"
],
"offsets": [
[
1374,
1399
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": ""
}
]
},
{
"id": "999793f0-f917-405b-9fa9-0c1c679678aa",
"type": "variant",
"text": [
"(ACG --> ACA) in codon 594"
],
"offsets": [
[
1531,
1557
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2228480"
}
]
},
{
"id": "eea8e878-5a6c-4560-9f2a-e56fb1668569",
"type": "variant",
"text": [
"codon 325 (CCC --> CCG)"
],
"offsets": [
[
1736,
1759
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801132"
}
]
},
{
"id": "6c6458d3-ac7a-40ac-a773-645c6bc0f8b2",
"type": "variant",
"text": [
"codon 594"
],
"offsets": [
[
1548,
1557
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2228480"
}
]
}
] | [] | [] | [] |
69 | 15084933 | [
{
"id": "e955b87c-981b-4813-bada-975050225715",
"type": "title",
"text": [
"Cytokines and chronic rejection: a study in kidney transplant long-term survivors."
],
"offsets": [
[
0,
82
]
]
},
{
"id": "52a20a39-e829-4fc3-a0d2-da6382ed06f8",
"type": "abstract",
"text": [
"BACKGROUND: In part, the long-term survival of kidney transplants depends on the efforts to perform grafts with good human leukocyte antigen (HLA) compatibility, but there are other mechanisms that must induce some sort of tolerance and impair the anti-graft immune reaction. Because cytokines are one of the main components of immune response, we evaluated single nucleotide polymorphisms (SNPs) of several cytokine genes that may influence the production of a given cytokine and therefore the features of immune reactions. METHODS: A total of 416 first cadaveric kidney transplants were monitored for HLA matching. After 10 years, the graft was still functional in 171 of 416 patients; 102 of 171 patients were also typed for cytokine polymorphisms. RESULTS: The mismatch distributions in patients who underwent transplantation were not statistically different from the entire group of patients who underwent transplantation during the same time period. Moreover, it seems that almost all of the HLA class I incompatible long-term survivors are homozygous for GG at the -1082 interleukin (IL)-10 or CC at the -33IL4 . CONCLUSIONS: We observed that a match for class I and class II HLA antigens apparently does not favor the long-term survival of transplanted kidneys. In fact, matched grafts are lost before 10 years in the same proportion as the mismatched grafts. We also demonstrated (1) that patients who are homozygous for GG at the SNP -1082IL10 (high IL-10 producers) and HLA class I mismatched (but matched for class II) are protected from chronic rejection, and (2) that patients who are homozygous for CC at the SNP -33IL4 (low IL-4 producers) and HLA class I mismatched (regardless of matching for class II) are protected from chronic rejection."
],
"offsets": [
[
83,
1866
]
]
}
] | [
{
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"human leukocyte antigen (HLA)"
],
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[
201,
230
]
],
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"db_id": "No"
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]
},
{
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"text": [
"HLA"
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226,
229
]
],
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"db_id": "No"
}
]
},
{
"id": "e778915b-3c9a-469a-80c0-fad53299aab3",
"type": "gene",
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"HLA"
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226,
229
]
],
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]
},
{
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"type": "gene",
"text": [
"interleukin (IL)-10"
],
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[
1170,
1189
]
],
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"db_id": "3586"
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]
},
{
"id": "59dddf35-a05b-4754-a1f6-c70bff0c8183",
"type": "gene",
"text": [
"HLA"
],
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[
226,
229
]
],
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"db_id": "No"
}
]
},
{
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"type": "gene",
"text": [
"IL-10"
],
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[
1559,
1564
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],
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]
},
{
"id": "75b63c91-f337-468f-a9c7-7af5df6cf929",
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"text": [
"HLA"
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[
226,
229
]
],
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{
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"db_id": "No"
}
]
},
{
"id": "b11e5af0-2cad-40ca-be4e-143fa5f07e6f",
"type": "gene",
"text": [
"IL-4"
],
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[
1745,
1749
]
],
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"db_id": "3565"
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]
},
{
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"type": "gene",
"text": [
"HLA"
],
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226,
229
]
],
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{
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"db_id": "No"
}
]
},
{
"id": "0395827d-6af8-475e-a5e6-9744672467af",
"type": "variant",
"text": [
"GG at the -1082"
],
"offsets": [
[
1152,
1167
]
],
"normalized": [
{
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"db_id": "G-1082G"
}
]
},
{
"id": "44815565-b222-4d90-93a2-4d77527a9d61",
"type": "variant",
"text": [
"CC at the -33IL4"
],
"offsets": [
[
1195,
1211
]
],
"normalized": [
{
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"db_id": "C-33C"
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]
},
{
"id": "4ba3bb69-5a77-400a-925e-b8f5edf2296f",
"type": "variant",
"text": [
"-1082IL10"
],
"offsets": [
[
1541,
1550
]
],
"normalized": [
{
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]
},
{
"id": "3e60da39-83e9-467b-a75f-50d6d22d67a1",
"type": "variant",
"text": [
"-33IL4"
],
"offsets": [
[
1205,
1211
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
}
] | [] | [] | [] |
70 | 15087412 | [
{
"id": "ac371128-b400-4871-b076-afabc47191a5",
"type": "title",
"text": [
"Sequence variants of toll-like receptor 4 are associated with prostate cancer risk: results from the CAncer Prostate in Sweden Study."
],
"offsets": [
[
0,
135
]
]
},
{
"id": "64f62c77-7cb4-4131-a7ec-832d13c6b443",
"type": "abstract",
"text": [
"Inflammation has been implicated as an etiological factor in several human cancers. Growing evidence suggests that chronic inflammation may also play a role in the etiology of prostate cancer. Considering that genetic susceptibility is a major risk factor for this disease, we hypothesize that sequence variants in genes that regulate inflammation may modify individual susceptibility to prostate cancer. The lipopolysaccharide receptor Toll-like receptor 4 ( TLR4 ) is a central player in the signaling pathways of the innate immune response to infection by Gram-negative bacteria and is an important candidate inflammatory gene. We performed a systematic genetic analysis of TLR4 sequence variants by evaluating eight single-nucleotide polymorphisms that span the entire gene among 1383 newly diagnosed prostate cancer patients and 780 age- and residence-matched controls in Sweden. We found an association between a sequence variant ( 11381G/C ) in the 3'-untranslated region of the TLR4 gene and prostate cancer risk. The frequency of the variant genotypes (CG or CC) was significantly higher in the patients (24.1%) than in the controls (19.7%; P = 0.02). The frequency of risk genotypes among patients diagnosed before the age of 65 years was even higher (26.3%). Compared with men who had the wild-type genotype of this single-nucleotide polymorphism (GG), those with GC or CC genotypes had a 26% increased risk for prostate cancer (odds ratio, 1.26; 95% confidence interval, 1.01-1.57) and 39% increased risk increased risk for early onset prostate cancer (before age 65 years; odds ratio, 1.39; 95% confidence interval, 1.02-1.91). The risk attributable to this variant for prostate cancer in Sweden was estimated to be 4.9%. Although the biological mechanism of the observed association remains to be elucidated, our finding supports a role for a bacteria-associated response pathway, possibly acting via inflammation, in the development of prostate cancer."
],
"offsets": [
[
136,
2109
]
]
}
] | [
{
"id": "5031beda-115a-404f-918e-e3c47e93b075",
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"Toll-like receptor 4"
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[
574,
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],
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"db_name": "NCBI Gene",
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]
},
{
"id": "2b941557-f5d0-438c-adb4-afde356baf2a",
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"TLR4"
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598,
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]
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]
},
{
"id": "73096179-a459-442b-bcc2-9a21269dee49",
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"TLR4"
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]
},
{
"id": "fb888cec-1463-4236-a952-9b2a68d9c091",
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"TLR4"
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598,
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],
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}
]
},
{
"id": "4b5d1470-c215-4c40-bbe5-d81029f111b1",
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"text": [
"11381G/C"
],
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[
1078,
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]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G11381C"
}
]
}
] | [] | [] | [] |
71 | 15091315 | [
{
"id": "f95126b6-c239-4182-b1b3-df9a3fd5355d",
"type": "title",
"text": [
"Is NOTCH4 associated with schizophrenia?"
],
"offsets": [
[
0,
42
]
]
},
{
"id": "a108035c-65e5-40c1-a194-0b1dd44a92e2",
"type": "abstract",
"text": [
"The NOTCH4 locus was reported to be associated with schizophrenia in our previous study but the subsequent replication by other workers has been inconsistent. To find out possible reasons for the poor replication, the present work was undertaken to analyse four functional single nucleotide polymorphisms (SNPs) ( rs367398 , rs915894 , rs520692 and rs422951 ) at the NOTCH4 locus among 141 schizophrenic family trios of Chinese Han descent. Of these four SNPs, rs520692 was the only one associated with schizophrenia (P = 0.017); the other three, however, did not show any association with the illness, including rs367398 located in the promoter region, which had shown a strong association with the illness in our previous study conducted with British samples. Although these four SNPs analysed lie within a less than 4 kb segment of genomic DNA, the pattern of linkage disequilibrium between them was unexpected. The strongest linkage disequilibrium was shown only between rs367398 and rs520692 and between rs520692 and rs422951 in both parent and patient groups. This study raises the possibility that there might be two or more disease-underlying variants at the NOTCH4 locus or at a nearby locus, and that the allelic or locus heterogeneity may be one of the possible reasons for the poor replication of the NOTCH4 finding."
],
"offsets": [
[
43,
1395
]
]
}
] | [
{
"id": "5253b61b-aebf-44cf-b5e5-17c324ad09fa",
"type": "gene",
"text": [
"NOTCH4"
],
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[
4,
10
]
],
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}
]
},
{
"id": "ca10c168-204e-4151-bf68-67e2e2fc2074",
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"NOTCH4"
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"NOTCH4"
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},
{
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"rs367398"
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"rs915894"
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]
},
{
"id": "f3b5d3e3-a6e7-4bb2-bf63-109913580fdb",
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"rs520692"
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383,
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]
],
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]
},
{
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"rs422951"
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398,
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]
],
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]
},
{
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"rs520692"
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383,
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]
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{
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"rs367398"
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359,
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],
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]
},
{
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"rs367398"
],
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[
359,
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],
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}
]
},
{
"id": "d660798f-eb90-4b7f-82a3-50260a0985fa",
"type": "variant",
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"rs520692"
],
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383,
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]
],
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]
},
{
"id": "f40b3699-2b7f-42ee-aeb6-a31d691fae5f",
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"text": [
"rs520692"
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383,
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],
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]
},
{
"id": "5d386507-c43b-4f69-9d7e-c8168f4906d4",
"type": "variant",
"text": [
"rs422951"
],
"offsets": [
[
398,
406
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "422951"
}
]
}
] | [] | [] | [] |
72 | 15091317 | [
{
"id": "5be012fe-8fbe-44b4-b915-4e04958b58c5",
"type": "title",
"text": [
"No genetic association between tumour necrosis factor receptor II 196R polymorphism and Japanese sporadic Alzheimer's disease."
],
"offsets": [
[
0,
130
]
]
},
{
"id": "aaaf5d89-9746-4050-91a1-d3984c57bc9f",
"type": "abstract",
"text": [
"Recent studies have reported that acute effects of tumour necrosis factor (TNF) , a pro-inflammatory cytokine, are limited by binding to a soluble receptor, TNF receptor II , and the G allele at position 196 in exon 6 of the TNF receptor II gene (TNFRII 196R) gene ( TNFRII 196R ) has been associated with auto-immune diseases. Since complex interactions among cytokines have been suggested around senile plaques in Alzheimer's disease, TNF might be associated with ageing and the pathophysiology of Alzheimer's disease. We examined the TNFRII 196R polymorphism in 243 Japanese sporadic Alzheimer's disease cases and 106 control cases using a polymerase chain reaction-restriction fragment length polymorphism method. Allelic frequencies with TNFRII 196R T/G polymorphism were 28.3% and 27.4% in the control and Alzheimer's disease groups, respectively. The results showed no genetic association between TNFRII 196R polymorphism and Alzheimer's disease. The TNFRII 196R G allele does not appear to be associated with Alzheimer's disease susceptibility in a Japanese population."
],
"offsets": [
[
131,
1230
]
]
}
] | [
{
"id": "47e1938f-9637-4efd-be27-64cb3e83f4a1",
"type": "gene",
"text": [
"tumour necrosis factor (TNF)"
],
"offsets": [
[
183,
211
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "1a5df96c-4f91-40de-b335-67d8ff43372e",
"type": "gene",
"text": [
"TNF receptor II"
],
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290,
305
]
],
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"db_name": "NCBI Gene",
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}
]
},
{
"id": "e36370ad-f9da-49d5-b1a1-635d4a4c846c",
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"TNFRII"
],
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381,
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]
],
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}
]
},
{
"id": "bd06b514-ea95-4884-8294-b6a6de964ccd",
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"text": [
"TNFRII"
],
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381,
387
]
],
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}
]
},
{
"id": "b449325d-b831-4410-81d6-6be0aa9d35f2",
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"TNFRII"
],
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381,
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]
],
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]
},
{
"id": "0418c5fc-38e8-47b7-9a08-b2ccf7e40323",
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"TNFRII"
],
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381,
387
]
],
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}
]
},
{
"id": "a123ed4d-526c-4b52-a713-33937e9c7a40",
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"TNFRII"
],
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381,
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],
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}
]
},
{
"id": "5a3889cf-c7e6-476a-b731-d1c6658aef77",
"type": "variant",
"text": [
"G allele at position 196 in exon 6 of the TNF receptor II gene (TNFRII 196R)"
],
"offsets": [
[
317,
393
]
],
"normalized": [
{
"db_name": "dbSNP",
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}
]
},
{
"id": "29120d11-48d8-4b58-8be2-f1685d5100e7",
"type": "variant",
"text": [
"196R"
],
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69,
73
]
],
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]
},
{
"id": "7caac310-b639-486d-964c-a854f9dbce8c",
"type": "variant",
"text": [
"196R"
],
"offsets": [
[
69,
73
]
],
"normalized": [
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}
]
},
{
"id": "84aace8c-a1fd-459f-8e49-40f3d14e3799",
"type": "variant",
"text": [
"196R T/G"
],
"offsets": [
[
894,
902
]
],
"normalized": [
{
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"db_id": "1061622"
}
]
},
{
"id": "b9b9c93e-bc47-437a-9e37-e24127a6df3b",
"type": "variant",
"text": [
"196R"
],
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69,
73
]
],
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"db_id": "1061622"
}
]
},
{
"id": "dac73767-ba19-4fbc-8258-326b5c80a8dc",
"type": "variant",
"text": [
"196R G"
],
"offsets": [
[
1117,
1124
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1061622"
}
]
}
] | [] | [] | [] |
73 | 15094225 | [
{
"id": "a81570a3-5f41-4e21-9ae5-c0e11fbcc187",
"type": "title",
"text": [
"Polymorphisms of microsomal triglyceride transfer protein gene and manganese superoxide dismutase gene in non-alcoholic steatohepatitis."
],
"offsets": [
[
0,
140
]
]
},
{
"id": "b692a873-df36-4cf1-bb8c-b4d1f39b898a",
"type": "abstract",
"text": [
"BACKGROUND/AIMS: The pathogenesis of non-alcoholic steatohepatitis (NASH) is poorly understood. The aim of this study was to examine genetic influences on NASH pathogenesis. METHODS: Blood samples from 63 patients with biopsy-proven NASH and 150 healthy controls were analyzed by the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). Two functional polymorphisms were studied: the -493 G/T polymorphism in the promoter of microsomal triglyceride transfer protein (MTP) and the 1183 T/C polymorphism in the mitochondrial targeting sequence of manganese superoxide dismutase ( MnSOD ). RESULTS: NASH patients had a much higher incidence of the MTP gene G allele (P=0.001) and of the G/G genotype (P=0.002) compared to the controls. Fat occupied more area in liver lobules and the stage of NASH was advanced in patients with the G/G-genotype than in patients with G/T-genotype (P=0.04). NASH patients also had a higher incidence of the MnSOD T/T genotype (P=0.016). CONCLUSIONS: The G allele in the MTP promoter leads to decreased MTP transcription, less export of triglyceride from hepatocytes, and greater intracellular triglyceride accumulation. The T allele in MnSOD mitochondrial targeting sequence leads to less transport of MnSOD to the mitochondria. Therefore, functional polymorphisms in MTP and MnSOD may be involved in determining susceptibility of NASH."
],
"offsets": [
[
141,
1554
]
]
}
] | [
{
"id": "f2347c3e-7bec-491b-ab5e-a6fcd0a95200",
"type": "gene",
"text": [
"microsomal triglyceride transfer protein"
],
"offsets": [
[
18,
58
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4547"
}
]
},
{
"id": "13bf0297-41ef-4107-8b2a-6072f6dced18",
"type": "gene",
"text": [
"manganese superoxide dismutase"
],
"offsets": [
[
70,
100
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6648"
}
]
},
{
"id": "5affb87c-e73a-4442-8eca-f0dabcd646ff",
"type": "gene",
"text": [
"MnSOD"
],
"offsets": [
[
759,
764
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6648"
}
]
},
{
"id": "3a59e22e-72d0-4f59-b0f5-c5b5cd09d2a6",
"type": "gene",
"text": [
"MnSOD"
],
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[
759,
764
]
],
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"db_id": "6648"
}
]
},
{
"id": "5a8ca74c-560e-4230-837f-39cb33ba7cbb",
"type": "gene",
"text": [
"MnSOD"
],
"offsets": [
[
759,
764
]
],
"normalized": [
{
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"db_id": "6648"
}
]
},
{
"id": "c159dea7-ddfd-4d6f-b590-ea341b4eb9dc",
"type": "gene",
"text": [
"MnSOD"
],
"offsets": [
[
759,
764
]
],
"normalized": [
{
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"db_id": "6648"
}
]
},
{
"id": "302d7ebb-e780-4fa4-a631-45b7150558f9",
"type": "gene",
"text": [
"MnSOD"
],
"offsets": [
[
759,
764
]
],
"normalized": [
{
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"db_id": "6648"
}
]
},
{
"id": "4e395123-b68e-4cf3-aa26-d385a713eff8",
"type": "variant",
"text": [
"-493 G/T"
],
"offsets": [
[
558,
566
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1800591"
}
]
},
{
"id": "3c365998-3935-43b6-b2f8-1bd8f888b4ec",
"type": "variant",
"text": [
"1183 T/C"
],
"offsets": [
[
658,
666
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T1183C"
}
]
}
] | [] | [] | [] |
74 | 15099281 | [
{
"id": "ebb89a67-ecd4-4145-8100-a869bd20f1e9",
"type": "title",
"text": [
"The 894 G > T variant of endothelial nitric oxide synthase ( eNOS ) increases the risk of recurrent venous thrombosis through interaction with elevated homocysteine levels."
],
"offsets": [
[
0,
176
]
]
},
{
"id": "8afaf1dd-7407-4949-ae6e-096e7a432306",
"type": "abstract",
"text": [
"BACKGROUND: Venous thrombosis is a multicausal disease involving both genetic as well as acquired risk factors. Hyperhomocysteinemia is associated with a 2-fold increased risk of recurrent venous thrombosis (RVT). Recently, the 894 G > T variant of endothelial nitric oxide synthase ( eNOS ) was postulated to be associated with hyperhomocysteinemia. OBJECTIVES: We hypothesized an interrelation of hyperhomocysteinemia, the eNOS 894 G > T variant and RVT risk. METHODS: The eNOS 894 G > T variant was studied in 170 cases with a history of RVT and 433 controls from the general population. RESULTS: The eNOS 894 TT genotype may increase RVT risk [odds ratio (OR) 1.3 (0.7-2.6)], but no association of the eNOS 894 G > T variant with elevated homocysteine was found in controls. Interestingly, in RVT cases the coexistence of both the 894 TT genotype and elevated tHcy levels (> 90th percentile) was more frequently present than in controls, which led to a substantially increased risk of recurrent venous thrombosis [fasting tHcy OR 5.3 (1.1-24.1), postload tHcy OR 6.5 (1.6-29.5)]. CONCLUSION: The results of the present study demonstrate that the eNOS 894 G > T variation interacts with elevated tHcy levels, leading to an increased risk of recurrent thrombotic events. This interaction points in the direction of S-nitrosation as a mechanism by which homocysteine exerts its detrimental effects on the hemostatic system."
],
"offsets": [
[
177,
1627
]
]
}
] | [
{
"id": "f1aa89a6-92bb-4f9b-b06d-0529f913b3ba",
"type": "gene",
"text": [
"endothelial nitric oxide synthase"
],
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[
28,
61
]
],
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}
]
},
{
"id": "e79195b1-d612-4d5e-9eac-0d0f8614c40d",
"type": "gene",
"text": [
"eNOS"
],
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65,
69
]
],
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]
},
{
"id": "8a758149-7841-4d02-908d-5c0a01a2c4fc",
"type": "gene",
"text": [
"eNOS"
],
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],
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]
},
{
"id": "b0fd2d44-6a44-4d39-ad31-da8ea70b029a",
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],
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65,
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]
],
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]
},
{
"id": "9c9d4112-a09d-48ae-a8b8-20c36ae46273",
"type": "gene",
"text": [
"eNOS"
],
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[
65,
69
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4846"
}
]
},
{
"id": "01418683-5d4e-407c-9ae2-c2dcfd5c8a97",
"type": "gene",
"text": [
"eNOS"
],
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[
65,
69
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4846"
}
]
},
{
"id": "6da319c4-a455-40a7-ab08-1b0b4379ed7d",
"type": "gene",
"text": [
"eNOS"
],
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[
65,
69
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4846"
}
]
},
{
"id": "758dd234-3adc-4554-9f12-6d4820461f1c",
"type": "variant",
"text": [
"894 G > T"
],
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[
5,
14
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1799983"
}
]
},
{
"id": "0c6389d7-e3da-4da7-8a2e-d47b2ed8446f",
"type": "variant",
"text": [
"894 G > T"
],
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[
5,
14
]
],
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{
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"db_id": "1799983"
}
]
},
{
"id": "91aba655-5b19-4c21-b145-0db0723405a2",
"type": "variant",
"text": [
"894 G > T"
],
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[
5,
14
]
],
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{
"db_name": "dbSNP",
"db_id": "1799983"
}
]
},
{
"id": "e64f0398-c259-4632-a6d9-7d706248ce71",
"type": "variant",
"text": [
"894 TT"
],
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[
801,
807
]
],
"normalized": [
{
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}
]
},
{
"id": "cbdbfb9c-0146-45be-b4bc-a3f6b3c84e40",
"type": "variant",
"text": [
"894 G > T"
],
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[
5,
14
]
],
"normalized": [
{
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"db_id": "1799983"
}
]
},
{
"id": "f550525d-d92a-4dc1-bfc1-f98e7dbd5ba6",
"type": "variant",
"text": [
"894 TT"
],
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[
801,
807
]
],
"normalized": [
{
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"db_id": "1799983"
}
]
},
{
"id": "3c16c677-763d-44ce-9c9a-31fbbdc4031a",
"type": "variant",
"text": [
"894 G > T"
],
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[
5,
14
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1799983"
}
]
}
] | [] | [] | [] |
75 | 15099346 | [
{
"id": "6c6337c0-24c8-4134-a7ab-7be8b30d9c75",
"type": "title",
"text": [
"Association between -250G/A polymorphism of the hepatic lipase gene promoter and coronary artery disease and HDL-C levels in a Southern Brazilian population."
],
"offsets": [
[
0,
161
]
]
},
{
"id": "21fa11cc-30b5-4699-9c84-a7999ed6a693",
"type": "abstract",
"text": [
"Hepatic lipase (HL) is a glycoprotein that plays a major role in remodeling high-density lipoprotein (HDL). The effect of the -250G/A promoter polymorphism on coronary artery disease (CAD) and lipid levels was studied in 231 male CAD patients and in a population-based sample of men and women (n = 514). A sample of 140 men was chosen among those included in the population-based sample as controls for the CAD sample. In the total group of CAD patients, the frequency of the -250A allele was somewhat lower (25% in CAD patients and 32% in controls; p = 0.06), but when the control samples were compared only with the CAD(+) sample (more than 60% of luminal stenosis in at least one coronary artery or major branch segment) the -250A allele was significantly less frequent (23% in the patients vs 32% in controls; p = 0.02). A multiple logistic regression analysis showed that this association was independent of classical CAD risk factors [odds ratio (OR) = 1.79, p = 0.025]. Using multiple linear regression analyses, it has been shown that this polymorphism was a significant factor affecting HDL-C levels in men from the population-based sample (p = 0.001), an interaction between -250G/A variant and wine consumption was also detected (p = 0.001). Thus, our results show that the -250G/A polymorphism in the HL gene is associated with significant variations in HDL-C levels and CAD risk in males."
],
"offsets": [
[
162,
1574
]
]
}
] | [
{
"id": "2a94ca5d-8e3f-4de0-b9c2-d6c4f55fec7e",
"type": "gene",
"text": [
"Hepatic lipase (HL) "
],
"offsets": [
[
162,
182
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3990"
}
]
},
{
"id": "98b6c730-6cce-4863-a515-c5fa5b5bac52",
"type": "variant",
"text": [
"-250G/A"
],
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[
21,
28
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-250A"
}
]
},
{
"id": "3f19f6fd-f991-421f-994f-412fdffe10a8",
"type": "variant",
"text": [
"-250A"
],
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[
642,
647
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-250A"
}
]
},
{
"id": "03ebe24d-8164-48ec-814b-cfa56220a9cc",
"type": "variant",
"text": [
"-250A"
],
"offsets": [
[
642,
647
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-250A"
}
]
},
{
"id": "539bdb9e-f40f-4641-9136-810fc75f7deb",
"type": "variant",
"text": [
"-250G/A"
],
"offsets": [
[
21,
28
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-250A"
}
]
},
{
"id": "02fb89ee-7fe4-4a9a-b1fe-b4d4dd85fd55",
"type": "variant",
"text": [
"-250G/A"
],
"offsets": [
[
21,
28
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-250A"
}
]
}
] | [] | [] | [] |
76 | 15099969 | [
{
"id": "d94d8d5e-c1b0-427c-bfe4-9b7c1e7f1908",
"type": "title",
"text": [
"p53 and p21 genetic polymorphisms and susceptibility to endometrial cancer."
],
"offsets": [
[
0,
78
]
]
},
{
"id": "3bad624a-0a51-4ec0-a777-b6120e9e2ab6",
"type": "abstract",
"text": [
"OBJECTIVE: Recently, there has been considerable interest in the association of specific cancers with single nucleotide polymorphisms (SNPs). In this regard, genetic polymorphism at codon 72 (CCC/proline to CGC/arginine [Pro(72)Arg]) of the p53 gene is one of the most frequently studied subjects. An association between endometrial cancer and the polymorphism at codon 31 (AGC/serine to AGA/arginine [Ser(31)Arg]) of the p21 gene, which is known to be a downstream mediator of p53 , has also been reported. METHODS: The authors designed a hospital-based case-control study of 95 endometrial cancer patients and 285 non-cancer controls. For the determination of p53 and p21 polymorphism, allele-specific polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism assay was applied, respectively. RESULTS: We found statistically significant differences in the frequency of the p53 and p21 genotypes between these two groups (P < 0.001), respectively. The p53 genotypes containing the Pro allele were significantly associated with endometrial cancer with an odds ratio (OR) of 3.56 (95% confidence interval [CI] 2.10-6.04). Also, homozygous carriers of the p21 Ser allele showed a substantially increased risk of developing endometrial cancer (OR 2.68, 95% CI 1.59-4.51) as compared to homozygous and heterozygous carriers of the Arg allele. In addition, the combination of the pro allele containing genotypes of p53 and the Ser homozygous genotype of p21 posed a remarkably increased risk (OR 9.55, 95% CI 4.30-21.24) of endometrial cancer development. These significant differences were maintained throughout the groups after they were stratified by menopausal status. CONCLUSIONS: These data suggest that there is a significant association between the genetic polymorphisms of p53 , p21 , and specific combinations of the at-risk genotypes of these genes and the risk of developing endometrial cancer in Korean women."
],
"offsets": [
[
79,
2046
]
]
}
] | [
{
"id": "bb21ff1a-412f-44ab-9ec3-82cc2c940cc1",
"type": "gene",
"text": [
"p53"
],
"offsets": [
[
0,
3
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "8ef014dc-af3d-480d-8c67-8c2415fdbaf8",
"type": "gene",
"text": [
"p21"
],
"offsets": [
[
10,
13
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1026"
}
]
},
{
"id": "7c1ed359-94ba-486d-8352-f99862d6b8b8",
"type": "gene",
"text": [
"p53"
],
"offsets": [
[
0,
3
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "ba70cd73-9a5b-411f-b09d-21d6c4cfbe03",
"type": "gene",
"text": [
"p53"
],
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[
0,
3
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "7f36b25c-b067-4cb6-95ad-44ef3a030f30",
"type": "gene",
"text": [
"p21"
],
"offsets": [
[
10,
13
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1026"
}
]
},
{
"id": "05a3497e-3970-4d0a-b418-ae2e29a7999f",
"type": "gene",
"text": [
"p53"
],
"offsets": [
[
0,
3
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "5260a706-838d-47f6-a59b-63907cf1513c",
"type": "gene",
"text": [
"p21"
],
"offsets": [
[
10,
13
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1026"
}
]
},
{
"id": "c3d27391-8ddf-45f0-b19f-2507457bac30",
"type": "gene",
"text": [
"p53"
],
"offsets": [
[
0,
3
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "665eb0ba-29f5-4414-a3d1-6961feb6f886",
"type": "gene",
"text": [
"p21"
],
"offsets": [
[
10,
13
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1026"
}
]
},
{
"id": "6c681b33-b3ac-4c3c-97dc-25cfb865415c",
"type": "gene",
"text": [
"p53"
],
"offsets": [
[
0,
3
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "b1e08c20-03de-4033-9115-72b66fa8ea69",
"type": "gene",
"text": [
"p21"
],
"offsets": [
[
10,
13
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1026"
}
]
},
{
"id": "c5347a22-181a-4596-9654-69ea03589582",
"type": "gene",
"text": [
"p53"
],
"offsets": [
[
0,
3
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "cbb05700-6b43-4be2-8eff-2300c95b697f",
"type": "gene",
"text": [
"p21"
],
"offsets": [
[
10,
13
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1026"
}
]
},
{
"id": "08dc9c43-b60e-4edd-9b5b-cee049f54d87",
"type": "variant",
"text": [
"codon 72 (CCC/proline to CGC/arginine [Pro(72)Arg])"
],
"offsets": [
[
262,
313
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1042522"
}
]
},
{
"id": "860be15f-b35f-4ed1-bc1b-9b3cc6a6d6dd",
"type": "variant",
"text": [
"codon 31 (AGC/serine to AGA/arginine [Ser(31)Arg]) "
],
"offsets": [
[
448,
499
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801270"
}
]
}
] | [] | [] | [] |
77 | 15100460 | [
{
"id": "0fd314f6-7135-4bdb-9081-677078279396",
"type": "title",
"text": [
"Ethnic differences in polymorphisms of tumor necrosis factor-alpha , interleukin-10 , and transforming growth factor-beta1 genes in patients with chronic hepatitis C virus infection."
],
"offsets": [
[
0,
186
]
]
},
{
"id": "2cda5432-1431-405e-9eee-1a6c8e9055cc",
"type": "abstract",
"text": [
"Ethnic differences in the outcome of hepatitis C have been described. Our aim was to investigate ethnic differences in the distribution of genotypes associated with polymorphisms of the tumor necrosis factor-alpha promoter, interleukin-10 promoter, and transforming growth factor-beta1 leader sequence in patients with hepatitis C. Genomic DNA was obtained from 71 Egyptians and 67 Caucasians (hepatitis C and control patients). Amplification of appropriate gene segments was followed by direct sequencing. Infrequently occurring polymorphisms were identified at positions -244 and -77 of the tumor necrosis factor-alpha promoter and at positions -851 and -657 of the interleukin-10 promoter. The G/A genotype associated with tumor necrosis factor-alpha promoter positions -376 and -244 was more frequent in Egyptians (P =0.001 and P =0.004, respectively). The -244 G/A genotype occurred only in healthy Egyptians (P =0.024). Thus, ethnic differences in the distribution of genotypes of the tumor necrosis factor-alpha promoter exist, which may have clinical implications on the outcome of hepatitis C."
],
"offsets": [
[
187,
1305
]
]
}
] | [
{
"id": "21820833-b331-4ea2-acd0-d6481b1127cf",
"type": "gene",
"text": [
"tumor necrosis factor-alpha"
],
"offsets": [
[
40,
67
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "1c8bd0c8-926a-4519-a68e-f78fda6a1c46",
"type": "gene",
"text": [
"interleukin-10"
],
"offsets": [
[
71,
85
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3586"
}
]
},
{
"id": "ca807794-5057-4ebe-8d71-bcf39401044c",
"type": "gene",
"text": [
"transforming growth factor-beta1"
],
"offsets": [
[
93,
125
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7040"
}
]
},
{
"id": "7f2dd926-3872-4b73-b3af-146890196ea9",
"type": "gene",
"text": [
"tumor necrosis factor-alpha"
],
"offsets": [
[
40,
67
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "7987d604-a51c-4696-9721-86e2b25ebc67",
"type": "gene",
"text": [
"interleukin-10"
],
"offsets": [
[
71,
85
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3586"
}
]
},
{
"id": "a04dd15a-a9d4-4a5e-9036-d6c08c48d13a",
"type": "gene",
"text": [
"tumor necrosis factor-alpha"
],
"offsets": [
[
40,
67
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "c3c75c4b-afc1-4a4f-bafc-111103414bf7",
"type": "variant",
"text": [
"G/A genotype associated with tumor necrosis factor-alpha promoter positions -376 and -244"
],
"offsets": [
[
895,
984
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "f1772119-0f3f-433e-b856-4215b1c5fe65",
"type": "variant",
"text": [
"-244 G/A"
],
"offsets": [
[
1061,
1069
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-244A"
}
]
}
] | [] | [] | [] |
78 | 15101044 | [
{
"id": "d15fdd5e-602d-4462-8484-a3cec84728f6",
"type": "title",
"text": [
"Functional consequences of ATM sequence variants for chromosomal radiosensitivity."
],
"offsets": [
[
0,
84
]
]
},
{
"id": "5547d3a2-56ad-4f48-b037-ab6b7d6872f1",
"type": "abstract",
"text": [
"The ATM [for ataxia-telangiectasia (A-T) mutated] protein plays a key role in the detection and cellular response to DNA double-strand breaks. Several single-nucleotide polymorphisms (SNPs) have been described in the ATM gene; however, their association with cancer risk or radiosensitivity remains to be fully established. In this study, the functional consequences of specific ATM SNPs on in vitro radiosensitivity, as assessed by micronuclei (MN) formation, were measured in lymphoblastoid cell lines established from 10 breast cancer (BC) patients carrying different ATM missense SNPs, six A-T patients, six A-T heterozygotes (A-T het), and six normal individuals. The BC, A-T het, and A-T cell line groups showed significantly higher mean levels of MN formation after exposure to ionizing radiation (IR) than did the group containing normal cell lines, with similar levels in the BC and A-T het groups. Within the BC lines studied, the group composed of the six carrying the linked 2572T>C (858F>L) and 3161C>G (1054P>R) variants had a higher level of MN after IR exposure compared to that observed in the remaining four BC or in the normal cell lines. This increase was not related to the constitutive ATM mRNA level, which was similar in these BC and the normal cell lines. Our results indicate that alterations in the ATM gene, including the presence of heterozygous mutations and the 2572C and 3161G variant alleles, are associated with increased in vitro chromosomal radiosensitivity, perhaps by interfering with ATM function in a dominant-negative manner."
],
"offsets": [
[
85,
1669
]
]
}
] | [
{
"id": "ff07acfa-7bcc-4224-a2e6-fe48e54da310",
"type": "gene",
"text": [
"ATM [for ataxia-telangiectasia (A-T) mutated]"
],
"offsets": [
[
90,
135
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "472"
}
]
},
{
"id": "b0123013-0d0f-4d9b-84e4-d454803c8efa",
"type": "gene",
"text": [
"ATM"
],
"offsets": [
[
28,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "472"
}
]
},
{
"id": "fc1dd75a-69f6-4144-a006-eda5ed0010bb",
"type": "gene",
"text": [
"ATM"
],
"offsets": [
[
28,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "472"
}
]
},
{
"id": "c4a00323-1031-4cd2-92ee-262282d5c783",
"type": "gene",
"text": [
"ATM"
],
"offsets": [
[
28,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "472"
}
]
},
{
"id": "b30d8134-6559-4ae0-b770-25c905b6fc8f",
"type": "gene",
"text": [
"ATM"
],
"offsets": [
[
28,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "472"
}
]
},
{
"id": "8a841378-6e9d-4a1c-b130-42d08dde05eb",
"type": "gene",
"text": [
"ATM"
],
"offsets": [
[
28,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "472"
}
]
},
{
"id": "fb0df074-06dc-4803-867d-332ac802166a",
"type": "gene",
"text": [
"ATM"
],
"offsets": [
[
28,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "472"
}
]
},
{
"id": "049c2455-4c76-4e59-b420-94e32031bc60",
"type": "variant",
"text": [
"2572T>C (858F>L) "
],
"offsets": [
[
1081,
1098
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1800056"
}
]
},
{
"id": "1e573b6e-058c-4613-958f-9a5517736dbb",
"type": "variant",
"text": [
"3161C>G (1054P>R)"
],
"offsets": [
[
1104,
1121
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1800057"
}
]
}
] | [] | [] | [] |
79 | 15102677 | [
{
"id": "bdea02b4-e4e8-4754-b4ad-2bcb41fdeffb",
"type": "title",
"text": [
"Predictive models for breast cancer susceptibility from multiple single nucleotide polymorphisms."
],
"offsets": [
[
0,
97
]
]
},
{
"id": "199ec53e-72fa-4d72-a865-1ae29313358d",
"type": "abstract",
"text": [
"Hereditary predisposition and causative environmental exposures have long been recognized in human malignancies. In most instances, cancer cases occur sporadically, suggesting that environmental influences are critical in determining cancer risk. To test the influence of genetic polymorphisms on breast cancer risk, we have measured 98 single nucleotide polymorphisms (SNPs) distributed over 45 genes of potential relevance to breast cancer etiology in 174 patients and have compared these with matched normal controls. Using machine learning techniques such as support vector machines (SVMs), decision trees, and naive Bayes, we identified a subset of three SNPs as key discriminators between breast cancer and controls. The SVMs performed maximally among predictive models, achieving 69% predictive power in distinguishing between the two groups, compared with a 50% baseline predictive power obtained from the data after repeated random permutation of class labels (individuals with cancer or controls). However, the simpler naive Bayes model as well as the decision tree model performed quite similarly to the SVM. The three SNP sites most useful in this model were (a) the +4536T/C site of the aldosterone synthase gene CYP11B2 at amino acid residue 386 Val/Ala (T/C) (rs4541) ; (b) the +4328C/G site of the aryl hydrocarbon hydroxylase CYP1B1 at amino acid residue 293 Leu/Val (C/G) (rs5292) ; and (c) the +4449C/T site of the transcription factor BCL6 at amino acid 387 Asp/Asp (rs1056932) . No single SNP site on its own could achieve more than 60% in predictive accuracy. We have shown that multiple SNP sites from different genes over distant parts of the genome are better at identifying breast cancer patients than any one SNP alone. As high-throughput technology for SNPs improves and as more SNPs are identified, it is likely that much higher predictive accuracy will be achieved and a useful clinical tool developed."
],
"offsets": [
[
98,
2045
]
]
}
] | [
{
"id": "669b5b2c-12f7-4f64-b589-53c81a95b0b7",
"type": "gene",
"text": [
"CYP11B2"
],
"offsets": [
[
1327,
1334
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1584"
}
]
},
{
"id": "0be178cd-cc0f-4ec3-896e-1910f2a00226",
"type": "gene",
"text": [
"CYP1B1"
],
"offsets": [
[
1449,
1455
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1545"
}
]
},
{
"id": "bf08dfe9-c780-4615-b453-e4f373385244",
"type": "gene",
"text": [
"BCL6"
],
"offsets": [
[
1566,
1570
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "604"
}
]
},
{
"id": "0fcf7fb0-8391-4920-aa7f-c3f959b409aa",
"type": "variant",
"text": [
"+4536T/C"
],
"offsets": [
[
1278,
1286
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "4541"
}
]
},
{
"id": "0830606f-6da3-4e57-92d3-f8418b11b0ce",
"type": "variant",
"text": [
"386 Val/Ala (T/C) (rs4541)"
],
"offsets": [
[
1359,
1385
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "4541"
}
]
},
{
"id": "29518ada-c238-460a-a853-71a7dc1e2939",
"type": "variant",
"text": [
"+4328C/G"
],
"offsets": [
[
1397,
1405
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5292"
}
]
},
{
"id": "92db24a5-6681-49e7-bbb9-116686dfc298",
"type": "variant",
"text": [
"293 Leu/Val (C/G) (rs5292)"
],
"offsets": [
[
1480,
1506
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5292"
}
]
},
{
"id": "7b95da20-4691-4505-b18e-703af9525edb",
"type": "variant",
"text": [
"+4449C/T"
],
"offsets": [
[
1522,
1530
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1056932"
}
]
},
{
"id": "72c712d6-92da-40dd-bf05-0e84b90c34ae",
"type": "variant",
"text": [
"387 Asp/Asp (rs1056932)"
],
"offsets": [
[
1587,
1610
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1056932"
}
]
}
] | [] | [] | [] |
80 | 15103710 | [
{
"id": "508b4197-20f3-4834-ac8c-f3ba889ff80f",
"type": "title",
"text": [
"Association between nonsyndromic cleft lip with or without cleft palate and the glutamic acid decarboxylase 67 gene in the Japanese population."
],
"offsets": [
[
0,
145
]
]
},
{
"id": "ef5e8e0d-f01b-4cf2-9b4b-e91b3c8d2ee3",
"type": "abstract",
"text": [
"Nonsyndromic cleft lip with or without cleft palate (NSCLP) is one of the most common craniofacial malformations. Both genetic and environmental factors are involved in the pathogenesis. In addition to its role as an inhibitory neurotransmitter, gamma-aminobutyric acid (GABA) synthesized by glutamic acid decarboxylase (GAD) is presumed to play a role in normal embryonic, especially facial, development. This notion has been substantiated by the fact that Gad67 knockout mice have been shown to have cleft palate. We hypothesized that GAD67 may be involved in the development of NSCLP and investigated the possible association between the GAD67 gene ( GAD67 ) and NSCLP in Japanese patients. We screened 50 probands for single nucleotide polymorphisms (SNPs) in GAD67 using denaturing high performance liquid chromatography (DHPLC) and found seven SNPs. Since two SNPs showed complete linkage disequilibrium (LD) to the other SNPs, we constructed a 5-locus haplotype of GAD67 . The frequency distribution of the haplotype differed between NSCLP patients and controls (P = 0.0028). The frequency of -445A , -292A , -147G , 111C , and IVS9-39T haplotype in the NSCLP patients was significantly lower than that in controls (P = 0.00098). In a transmission disequilibrium test (TDT) in 99 parent-offspring trios, we found -445C , -292C , -147G , 111C , and IVS9-39C haplotype was preferentially transmitted to the patients with cleft lip and palate (P = 0.0077). Our data suggest that GAD67 is involved in the pathogenesis of NSCLP in the Japanese population."
],
"offsets": [
[
146,
1724
]
]
}
] | [
{
"id": "45c76b8a-fecb-43f8-b242-987793bfb1af",
"type": "gene",
"text": [
"GAD67"
],
"offsets": [
[
684,
689
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2571"
}
]
},
{
"id": "5151a41f-99f8-428d-9240-f4b1e6c51de0",
"type": "gene",
"text": [
"GAD67"
],
"offsets": [
[
684,
689
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2571"
}
]
},
{
"id": "fcfa1b78-5d95-434a-8a9a-bad49c887eb2",
"type": "gene",
"text": [
"GAD67"
],
"offsets": [
[
684,
689
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2571"
}
]
},
{
"id": "85280d3d-1508-4a65-8d98-c3cb31e5f312",
"type": "gene",
"text": [
"GAD67"
],
"offsets": [
[
684,
689
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2571"
}
]
},
{
"id": "32ceccef-22fa-4dab-b71e-e36696629928",
"type": "gene",
"text": [
"GAD67"
],
"offsets": [
[
684,
689
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2571"
}
]
},
{
"id": "cde1fb67-9ead-4c90-91a0-97e70a5dc43a",
"type": "gene",
"text": [
"GAD67"
],
"offsets": [
[
684,
689
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2571"
}
]
},
{
"id": "fe110923-9529-466c-a752-cab9922c7929",
"type": "variant",
"text": [
"-445A"
],
"offsets": [
[
1254,
1259
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-445A"
}
]
},
{
"id": "d024dd33-b55a-4d2d-94b1-6d565d5292a0",
"type": "variant",
"text": [
"-292A"
],
"offsets": [
[
1263,
1268
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-292A"
}
]
},
{
"id": "49f32572-f6b2-4c30-b0f5-1e592a430991",
"type": "variant",
"text": [
"-147G"
],
"offsets": [
[
1272,
1277
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-147G"
}
]
},
{
"id": "c1a1700c-8b66-436c-a8c5-b6f605758f69",
"type": "variant",
"text": [
"111C"
],
"offsets": [
[
1281,
1285
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "11542313"
}
]
},
{
"id": "87138e55-a9af-4d77-beeb-fdf98feef792",
"type": "variant",
"text": [
"IVS9-39T"
],
"offsets": [
[
1293,
1301
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "701492"
}
]
},
{
"id": "bdcd2ea8-d71e-4e7d-98bf-4024ef8c0015",
"type": "variant",
"text": [
"-445C"
],
"offsets": [
[
1480,
1485
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-445C"
}
]
},
{
"id": "67557a90-b3b2-48b6-a76c-fb02e49db471",
"type": "variant",
"text": [
"-292C"
],
"offsets": [
[
1489,
1494
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-292C"
}
]
},
{
"id": "24128efd-6a11-4585-9ec3-9af3d073a3be",
"type": "variant",
"text": [
"-147G"
],
"offsets": [
[
1272,
1277
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-147G"
}
]
},
{
"id": "816c61a4-e840-4d43-b1a5-ee701fbc9da1",
"type": "variant",
"text": [
"111C"
],
"offsets": [
[
1281,
1285
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "11542313"
}
]
},
{
"id": "5d290b55-e42c-4f9a-8911-a968d3c89ddf",
"type": "variant",
"text": [
"IVS9-39C"
],
"offsets": [
[
1519,
1527
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "701492"
}
]
}
] | [] | [] | [] |
81 | 15108194 | [
{
"id": "1b0a66b7-7545-4438-8279-eb0400ecfde4",
"type": "title",
"text": [
"Association between the brain-derived neurotrophic factor 196G/A polymorphism and eating disorders."
],
"offsets": [
[
0,
103
]
]
},
{
"id": "ae44951c-9359-41cb-ab82-b705785c6387",
"type": "abstract",
"text": [
"Several lines of evidence suggest that genetic factors might contribute to the pathogenesis of eating disorders and that brain-derived neurotrophic factor ( BDNF ) plays a role in the pathophysiology of eating disorders. To investigate the role of the BDNF gene in the susceptibility to eating disorders, we analyzed the BDNF 196G/A gene polymorphism in female patients with eating disorders and female normal controls. The difference in the genotype frequency between patients (n = 198) and normal controls (n = 222) was statistically significant (P = 0.029). Interestingly, a significant (P = 0.015) difference in the genotype frequency between normal controls and bulimia nervosa patients (n = 101) with binge-purging type was detected. This study suggests that the BDNF 196G/A gene polymorphism might be associated with a susceptibility to eating disorders.Copyright 2003 Wiley-Liss, Inc."
],
"offsets": [
[
104,
1008
]
]
}
] | [
{
"id": "4f196f78-f991-4534-a5c1-b99c1c105017",
"type": "gene",
"text": [
"brain-derived neurotrophic factor"
],
"offsets": [
[
25,
58
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "627"
}
]
},
{
"id": "1fadb3e3-d3fe-4c78-abfd-c8bc25c45364",
"type": "gene",
"text": [
"BDNF"
],
"offsets": [
[
263,
267
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "627"
}
]
},
{
"id": "8fa7d2d8-cd6d-4e7b-81be-ebbbb6a8801c",
"type": "gene",
"text": [
"BDNF"
],
"offsets": [
[
263,
267
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "627"
}
]
},
{
"id": "a3731dd5-bf63-426a-a93d-f8b70bd801c6",
"type": "gene",
"text": [
"BDNF"
],
"offsets": [
[
263,
267
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "627"
}
]
},
{
"id": "cc06fb6a-c397-4a07-8ae7-dbcc445b455c",
"type": "gene",
"text": [
"BDNF"
],
"offsets": [
[
263,
267
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "627"
}
]
},
{
"id": "aa7d06c1-2898-4a7e-bd10-4f258157a7c9",
"type": "variant",
"text": [
"196G/A"
],
"offsets": [
[
61,
67
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "6265"
}
]
},
{
"id": "1dd889d2-86aa-4270-b6e3-52ce3adc5b5a",
"type": "variant",
"text": [
"196G/A"
],
"offsets": [
[
61,
67
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "6265"
}
]
}
] | [] | [] | [] |
82 | 15108283 | [
{
"id": "67ba69a1-4d7e-4a1e-876e-5dda65a7c57b",
"type": "title",
"text": [
"Human vitamin K-dependent GAS6 : gene structure, allelic variation, and association with stroke."
],
"offsets": [
[
0,
97
]
]
},
{
"id": "8ddd21b0-dc1b-4d4e-9abf-5c96196f25b7",
"type": "abstract",
"text": [
"The product of the growth arrest-specific gene 6 ( GAS6 ), a ligand for the Axl , Sky , and Mer tyrosine kinase receptors, is a vitamin K-dependent protein, structurally related to anticoagulant protein S. Gas6-deficient mice are protected against thrombosis, demonstrating the importance of this protein in the cardiovascular system. The present study was aimed at determining the human GAS6 intron-exon structure and analyzing the gene for the presence of allelic variants that could be associated with atherothrombotic disease. Online analyses allowed us to localize 15 GAS6 exons and to determine the sequence of their intron-flanking regions, in a chromosome 13 region spanning 43.8 kb of DNA. SSCP analysis of PCR-amplified GAS6 exons with their intron-flanking regions from a minimum of 12 control DNA samples, revealed the presence of eight different variants, which were confirmed to be single nucleotide polymorphisms (SNPs). Three of them ( c.1263G>C , c.1332C>T , and c.1869T>C ) are localized in exons 11, 12, and 14, and appear to be neutral since they do not modify the encoded amino acid. The other SNPs ( c.280+170C>G , c.712+26G>A , c.713-155C>T , c.834+7G>A , and c.1478-94C>G ) are in introns 3, 7, 8, and 12. A preliminary analysis of five of these SNPs in a group of 110 healthy controls and 188 patients with atherothrombotic disease has revealed statistically significant differences between controls and stroke patients in the allelic distributions of one of these variants ( c.834+7G>A in intron 8). The SNP identification in GAS6 reported here would be very useful in future association studies aimed at determining the physiologic role of GAS6 in stroke and other human diseases."
],
"offsets": [
[
98,
1828
]
]
}
] | [
{
"id": "2c6c51af-dd57-4272-ad6f-28f5353f46a1",
"type": "gene",
"text": [
"growth arrest-specific gene 6"
],
"offsets": [
[
118,
147
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2621"
}
]
},
{
"id": "58018137-23a6-43b3-99eb-161d43ec30af",
"type": "gene",
"text": [
"GAS6"
],
"offsets": [
[
27,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2621"
}
]
},
{
"id": "6ea3cb63-3580-4b50-962f-3600a9b7233a",
"type": "gene",
"text": [
"Axl"
],
"offsets": [
[
177,
180
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "558"
}
]
},
{
"id": "1cc652c3-9f6c-4ece-9f9c-fef0a8eb5601",
"type": "gene",
"text": [
"Sky"
],
"offsets": [
[
184,
187
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7301"
}
]
},
{
"id": "173dcf43-d5d1-490c-8464-3df58fd6d13d",
"type": "gene",
"text": [
"Mer"
],
"offsets": [
[
195,
198
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "10461"
}
]
},
{
"id": "a2dc09b8-a57c-40dd-b535-3d0b77244bf8",
"type": "gene",
"text": [
"GAS6"
],
"offsets": [
[
27,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2621"
}
]
},
{
"id": "0be70fd7-fc6b-4b35-8fad-ea4e49ee88f2",
"type": "gene",
"text": [
"GAS6"
],
"offsets": [
[
27,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2621"
}
]
},
{
"id": "ff923a9c-df77-4004-bca1-ab6b684cac64",
"type": "gene",
"text": [
"GAS6"
],
"offsets": [
[
27,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2621"
}
]
},
{
"id": "44f7f418-ac4f-4078-b6c9-72e198f47304",
"type": "gene",
"text": [
"GAS6"
],
"offsets": [
[
27,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2621"
}
]
},
{
"id": "a9c951ef-4a57-4b29-a186-025ba6a0821f",
"type": "gene",
"text": [
"GAS6"
],
"offsets": [
[
27,
31
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2621"
}
]
},
{
"id": "c9e9d50c-0ae0-417e-a0a9-28ecd52f6449",
"type": "variant",
"text": [
"c.1263G>C"
],
"offsets": [
[
1062,
1071
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "8191975"
}
]
},
{
"id": "ef616368-e368-4515-85ba-114760a4b89b",
"type": "variant",
"text": [
"c.1332C>T"
],
"offsets": [
[
1075,
1084
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1803628"
}
]
},
{
"id": "4b530b9f-7adb-4156-815d-48f481809ab6",
"type": "variant",
"text": [
"c.1869T>C"
],
"offsets": [
[
1092,
1101
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "7400002"
}
]
},
{
"id": "894c25cd-a4a8-485c-b9fd-caddafd31f9f",
"type": "variant",
"text": [
"c.280+170C>G"
],
"offsets": [
[
1234,
1246
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C280+170G"
}
]
},
{
"id": "95e7ab79-77af-4ec5-bbee-8817baa8dbc0",
"type": "variant",
"text": [
"c.712+26G>A"
],
"offsets": [
[
1250,
1261
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G712+26A"
}
]
},
{
"id": "7131ae93-498b-4315-a0d5-f605a8b454ab",
"type": "variant",
"text": [
"c.713-155C>T"
],
"offsets": [
[
1265,
1277
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C713-155T"
}
]
},
{
"id": "7adc95cd-6db0-4ab7-9e5a-e9047c98d333",
"type": "variant",
"text": [
"c.834+7G>A"
],
"offsets": [
[
1281,
1291
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G834+7A"
}
]
},
{
"id": "0a0099e1-f683-4818-8529-3972ba33255f",
"type": "variant",
"text": [
"c.1478-94C>G"
],
"offsets": [
[
1299,
1311
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C1478-94G"
}
]
},
{
"id": "c4938826-6e07-49cf-9876-b9f47ff38b2d",
"type": "variant",
"text": [
"c.834+7G>A"
],
"offsets": [
[
1281,
1291
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G834+7A"
}
]
}
] | [] | [] | [] |
83 | 15110318 | [
{
"id": "84d9938a-bcfd-40db-8102-380c06412388",
"type": "title",
"text": [
"Human mitochondrial transcription factor B1 as a modifier gene for hearing loss associated with the mitochondrial A1555G mutation."
],
"offsets": [
[
0,
133
]
]
},
{
"id": "14aac224-f23b-447d-abd8-daebc379d1d1",
"type": "abstract",
"text": [
"Phenotypic expression of the deafness-associated homoplasmic A1555G mutation in the mitochondrial 12S rRNA gene varies from profound congenital hearing loss to normal hearing. It has been shown that this variability in clinical expression in most patients is due to the complex inheritance of multiple nuclear-encoded modifier genes. Human mitochondrial transcription factor B1 ( TFB1M ) has been proposed as a candidate for being such a modifier, since it methylates adenine residues in the adjacent loop of the A1555G mutation in the 12S rRNA gene. Polymorphic markers within and adjacent to the TFB1M gene were genotyped in 214 individuals from 41 multiplex families with the A1555G mutation of Spanish, Italian, and Arab-Israeli origin. Multipoint non-parametric linkage analysis of all families combined revealed an NPL score of 1.7 (P = 0.05), and a Lod score of 1.4 (P = 0.04). Linkage disequilibrium by the Transmission Disequilibrium Test at D6S1577 , a microsatellite adjacent to TFB1M , showed preferential non-transmission of an allele to affected individuals with chi2 = 8.76; P = 0.003. Sequence analysis of the coding region of the gene and testing of all intragenic SNPs did not reveal a putative causative mutation. These data provide suggestive evidence that TFB1M is a nuclear-encoded modifier gene for phenotypic expression of the A1555G mutation, and that the effect may occur through a regulatory or splicing mutation."
],
"offsets": [
[
134,
1592
]
]
}
] | [
{
"id": "4026efec-d502-4b43-9acf-be8ea3c9f154",
"type": "gene",
"text": [
"mitochondrial 12S rRNA"
],
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[
221,
243
]
],
"normalized": [
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"db_name": "NCBI Gene",
"db_id": "4549"
}
]
},
{
"id": "c54266ba-89be-4851-9643-87994783eb7c",
"type": "gene",
"text": [
"Human mitochondrial transcription factor B1"
],
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[
0,
43
]
],
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}
]
},
{
"id": "e9f22718-737c-40af-9197-ae2522222993",
"type": "gene",
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"TFB1M"
],
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520,
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]
],
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}
]
},
{
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"TFB1M"
],
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520,
525
]
],
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"db_id": "51106"
}
]
},
{
"id": "902080d2-8634-4ee6-bcc3-7d09926d34dd",
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"TFB1M"
],
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520,
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],
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]
},
{
"id": "7e95d874-bb9a-4e59-93cc-a8f5358a4b7e",
"type": "gene",
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"TFB1M"
],
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520,
525
]
],
"normalized": [
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}
]
},
{
"id": "bce8d6f7-9404-41cf-bb9f-62f88cdf4a48",
"type": "variant",
"text": [
"A1555G"
],
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[
116,
122
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A1555G"
}
]
},
{
"id": "eb0970c2-d59f-4104-92d4-04ecf9dd457e",
"type": "variant",
"text": [
"A1555G"
],
"offsets": [
[
116,
122
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A1555G"
}
]
},
{
"id": "4861e4bd-d354-40f1-bab1-6bafc25d981c",
"type": "variant",
"text": [
"A1555G"
],
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[
116,
122
]
],
"normalized": [
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"db_name": "HGVS-like",
"db_id": "A1555G"
}
]
},
{
"id": "cee88344-9197-4f55-aeb2-e204a60ea179",
"type": "variant",
"text": [
"D6S1577"
],
"offsets": [
[
1098,
1105
]
],
"normalized": [
{
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}
]
},
{
"id": "c01b0a65-a1c5-4ab9-a5f0-11648c495b18",
"type": "variant",
"text": [
"A1555G"
],
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116,
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]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A1555G"
}
]
}
] | [] | [] | [] |
84 | 15114532 | [
{
"id": "b6c3c29b-5d03-4091-b551-e0bc1a8c5ea7",
"type": "title",
"text": [
"Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection."
],
"offsets": [
[
0,
97
]
]
},
{
"id": "31ddf594-b2a8-48cd-b7c3-b26898efa6da",
"type": "abstract",
"text": [
"The hemoglobin E variant (HbE; ( beta )26Glu-->Lys) is concentrated in parts of Southeast Asia where malaria is endemic, and HbE carrier status has been shown to confer some protection against Plasmodium falciparum malaria. To examine the effect of natural selection on the pattern of linkage disequilibrium (LD) and to infer the evolutionary history of the HbE variant, we analyzed biallelic markers surrounding the HbE variant in a Thai population. Pairwise LD analysis of HbE and 43 surrounding biallelic markers revealed LD of HbE extending beyond 100 kb, whereas no LD was observed between non- HbE variants and the same markers. The inferred haplotype network suggests a single origin of the HbE variant in the Thai population. Forward-in-time computer simulations under a variety of selection models indicate that the HbE variant arose 1,240-4,440 years ago. These results support the conjecture that the HbE mutation occurred recently, and the allele frequency has increased rapidly. Our study provides another clear demonstration that a high-resolution LD map across the human genome can detect recent variants that have been subjected to positive selection."
],
"offsets": [
[
98,
1284
]
]
}
] | [
{
"id": "7c3b54fa-8029-49da-83e4-069ab4f58bd2",
"type": "gene",
"text": [
"HbE"
],
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[
125,
128
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3046"
}
]
},
{
"id": "f4ce5b48-459f-403a-b030-b5e10b03585d",
"type": "gene",
"text": [
"HbE"
],
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[
125,
128
]
],
"normalized": [
{
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"db_id": "3046"
}
]
},
{
"id": "dbb6b307-9264-4ebc-8255-c14d95bf3d26",
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"HbE"
],
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125,
128
]
],
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}
]
},
{
"id": "68b1427a-e1fe-4536-b129-474a9812ca8f",
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"HbE"
],
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[
125,
128
]
],
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}
]
},
{
"id": "b9b10b39-914d-433a-a91f-3b71ca3cd1c7",
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"text": [
"HbE"
],
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125,
128
]
],
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}
]
},
{
"id": "31abb81e-62a6-47b1-85f8-3afb80e804ab",
"type": "gene",
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"HbE"
],
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[
125,
128
]
],
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"db_name": "NCBI Gene",
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}
]
},
{
"id": "9075b775-a6f6-4c00-a729-db8a25290c8e",
"type": "gene",
"text": [
"HbE"
],
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[
125,
128
]
],
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{
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}
]
},
{
"id": "b8f87820-c9cf-49b2-8bbd-0a77025463e3",
"type": "gene",
"text": [
"HbE"
],
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[
125,
128
]
],
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{
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}
]
},
{
"id": "910f4375-6d42-45c2-abc7-0a3c9d32adcc",
"type": "gene",
"text": [
"HbE"
],
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[
125,
128
]
],
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{
"db_name": "NCBI Gene",
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}
]
},
{
"id": "cc480b97-78be-453b-bd17-c33125f51af8",
"type": "variant",
"text": [
"hemoglobin E variant (HbE; ( beta )26Glu-->Lys)"
],
"offsets": [
[
103,
150
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "E26K"
}
]
}
] | [] | [] | [] |
85 | 15115760 | [
{
"id": "6fe65a9e-cd48-423c-8144-a78aca610b4a",
"type": "title",
"text": [
"Association of BDNF with anorexia, bulimia and age of onset of weight loss in six European populations."
],
"offsets": [
[
0,
105
]
]
},
{
"id": "9d592dfc-1add-4505-b0da-68daa959352f",
"type": "abstract",
"text": [
"Several genes with an essential role in the regulation of eating behavior and body weight are considered candidates involved in the etiology of eating disorders (ED), but no relevant susceptibility genes with a major effect on anorexia nervosa (AN) or bulimia nervosa (BN) have been identified. Brain-derived neurotrophic factor ( BDNF ) has been implicated in the regulation of food intake and body weight in rodents. We previously reported a strong association of the Met66 allele of the Val66Met BDNF variant with restricting AN (ANR) and low minimum body mass index in Spanish patients. Another single nucleotide polymorphism located in the promoter region of the BDNF gene ( -270C>T ) showed lack of association with any ED phenotype. In order to replicate these findings in a larger sample, we performed a case-control study in 1142 Caucasian patients with ED consecutively recruited in six different centers from five European countries (France, Germany, Italy, Spain and UK) participating in the 'Factors in Healthy Eating' project. We have found that the Met66 variant is strongly associated to all ED subtypes (AN, ANR, binge-eating/purging AN and BN), and that the -270C BDNF variant has an effect on BN and late age at onset of weight loss. These are the first two variants associated with the pathophysiology of ED in different populations and support a role for BDNF in the susceptibility to aberrant eating behaviors."
],
"offsets": [
[
106,
1556
]
]
}
] | [
{
"id": "e542d71a-18bb-4af1-af03-45d73c22a8f6",
"type": "gene",
"text": [
"Brain-derived neurotrophic factor"
],
"offsets": [
[
402,
435
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "627"
}
]
},
{
"id": "f6ec5f4e-2828-4402-aeaf-b74dbb829a6a",
"type": "gene",
"text": [
"BDNF"
],
"offsets": [
[
16,
20
]
],
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{
"db_name": "NCBI Gene",
"db_id": "627"
}
]
},
{
"id": "8235bd10-5c9f-4f68-9654-f76156b320df",
"type": "gene",
"text": [
"BDNF"
],
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[
16,
20
]
],
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{
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}
]
},
{
"id": "d5f7498c-a44c-4022-8351-f56e17899449",
"type": "gene",
"text": [
"BDNF"
],
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[
16,
20
]
],
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{
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}
]
},
{
"id": "1549aba4-1826-461b-9aea-64871445d8e1",
"type": "gene",
"text": [
"BDNF"
],
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[
16,
20
]
],
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{
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"db_id": "627"
}
]
},
{
"id": "dfd09561-7ce5-46c5-ba36-af15bb3a87a7",
"type": "gene",
"text": [
"BDNF"
],
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[
16,
20
]
],
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{
"db_name": "NCBI Gene",
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}
]
},
{
"id": "92696bd9-45d4-46be-8429-adcb24c92c00",
"type": "variant",
"text": [
"Met66"
],
"offsets": [
[
579,
584
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "6265"
}
]
},
{
"id": "0520161a-bce4-4646-88ba-a319cb904404",
"type": "variant",
"text": [
"Val66Met"
],
"offsets": [
[
601,
609
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "6265"
}
]
},
{
"id": "4271e7b0-f5d6-4cb2-b62c-6ad0c1a54c50",
"type": "variant",
"text": [
"-270C>T"
],
"offsets": [
[
796,
803
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-270T"
}
]
},
{
"id": "f6d42b79-d6a1-446f-b280-df542c9d7a96",
"type": "variant",
"text": [
"Met66"
],
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[
579,
584
]
],
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}
]
},
{
"id": "c8f54830-1f2b-45dd-b0a2-6fff27ac345d",
"type": "variant",
"text": [
"-270C"
],
"offsets": [
[
796,
801
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-270C"
}
]
}
] | [] | [] | [] |
86 | 15116249 | [
{
"id": "ca427a27-e97e-4769-bc30-4fa25f7acb37",
"type": "title",
"text": [
"Association after linkage analysis indicates that homozygosity for the 46C-->T polymorphism in the F12 gene is a genetic risk factor for venous thrombosis."
],
"offsets": [
[
0,
159
]
]
},
{
"id": "9aae372a-f040-4336-ae34-14b8606bf5cb",
"type": "abstract",
"text": [
"In a family-based study called GAIT (Genetic Analysis of Idiopathic Thrombophilia) that included a genome-wide scan we demonstrated that a polymorphism ( 46C-->T ) in the F12 locus jointly influences variability of plasma (Factor XII) FXII levels and susceptibility to thrombotic disease. It then became germane to determine the prevalence of the 46C-->T polymorphism and its relative risk of thrombotic disease. We followed up evidence for genetic linkage with a case-control study, including 250 unrelated consecutive Spanish patients suffering from venous thrombotic disease and 250 Spanish subjects matched for sex and age as a controls. We measured FXII levels and genotyped the 46C-->T polymorphism, as well as a number of classical risk factors for thrombotic disease.We confirmed that individuals with different genotypes for this polymorphism showed significant differences in their FXII levels. Most importantly, the mutated T allele in the homozygous state (genotype T/T) was associated with an increased risk of thrombosis (adjusted OR of 4.82; 95% CI 1.5-15.6), suggesting that the polymorphism itself is an independent risk factor for venous thromboembolism. This study confirms that the 46C-->T polymorphism is a genetic risk factor for venous thrombosis in the Spanish population. In addition, our results confirm that a genome-wide scan coupled with a classical case-control association study is an extremely valuable approach to identify DNA variants that affect complex diseases."
],
"offsets": [
[
160,
1672
]
]
}
] | [
{
"id": "a88b99b7-9ee4-4bb7-8919-0e1ac6c8527f",
"type": "gene",
"text": [
"F12"
],
"offsets": [
[
102,
105
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2161"
}
]
},
{
"id": "4a658542-373b-4424-b39a-c260f0fb281e",
"type": "gene",
"text": [
"(Factor XII) FXII"
],
"offsets": [
[
385,
402
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "6b8ad44f-80a2-4b5c-b05d-7cb71a6a150a",
"type": "gene",
"text": [
"FXII"
],
"offsets": [
[
398,
402
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "214ea1ae-b347-4866-bda9-a6d0aa3af093",
"type": "gene",
"text": [
"FXII"
],
"offsets": [
[
398,
402
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "ca814bf7-03f8-487b-bd90-b75ebf34f931",
"type": "variant",
"text": [
"46C-->T"
],
"offsets": [
[
72,
79
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C46T"
}
]
},
{
"id": "bc032bd0-c096-4392-9db9-ead442bd038a",
"type": "variant",
"text": [
"46C-->T"
],
"offsets": [
[
72,
79
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C46T"
}
]
},
{
"id": "be968aa6-6104-41a0-b296-739ef292d328",
"type": "variant",
"text": [
"46C-->T"
],
"offsets": [
[
72,
79
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C46T"
}
]
},
{
"id": "ce793754-4549-436a-af36-a584091514b0",
"type": "variant",
"text": [
"46C-->T"
],
"offsets": [
[
72,
79
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C46T"
}
]
}
] | [] | [] | [] |
87 | 15116260 | [
{
"id": "ad66763c-c3d1-4532-8f30-c7d6bb1105cc",
"type": "title",
"text": [
"Pharmacogenetics of the CD14 endotoxin receptor polymorphism and progression of coronary atherosclerosis."
],
"offsets": [
[
0,
107
]
]
},
{
"id": "f03749d6-5c29-4f9c-809b-6a1a91b3c78a",
"type": "abstract",
"text": [
"Atherosclerosis is at least in part an inflammatory disease. CD14 is an endotoxin receptor that after binding of lipopolysaccharides evokes endothelial activation and secretion of several cytokines. A polymorphism of CD14 has been associated with myocardial infarction.We evaluated the role of the -159 T/C polymorphism in the promoter region of the CD14 gene in relation to severity and progression of coronary atherosclerosis and response to the HMG CoA reductase inhibitor pravastatin. We recruited patients from the multi-center double-blind randomized placebo controlled REGRESS trial and genotyped the -159T/C CD14 polymorphism. DNA and angiographic follow-up were available from 759 patients with objectivated coronary artery disease. We measured changes in mean segment diameter (MSD) and minimum obstruction diameter (MOD) with quantitative coronary angiography and noted the occurrence of major adverse cardiac events. The genotype distribution was 28% TT, 49% CT, 23% CC. We did not find any association between genotype and MSD and MOD at baseline, frequency of previous myocardial infarction, changes in MSD and MOD or major clinical events. Treatment with the HMG CoA reductase inhibitor pravastatin reduced progression of coronary atherosclerosis and adverse events equally for all genotypes. We conclude, that the -159T/C polymorphism in the CD14 monocyte receptor gene was not associated with progression of coronary atherosclerosis in this population nor did it influence the efficacy of pravastatin in the treatment of atherosclerosis."
],
"offsets": [
[
108,
1682
]
]
}
] | [
{
"id": "e088eb67-9e3f-4052-86f8-499683176e5c",
"type": "gene",
"text": [
"CD14"
],
"offsets": [
[
25,
29
]
],
"normalized": [
{
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"db_id": "929"
}
]
},
{
"id": "1bc68a62-c40f-4957-a8f8-107f0ebb4ea2",
"type": "gene",
"text": [
"CD14"
],
"offsets": [
[
25,
29
]
],
"normalized": [
{
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}
]
},
{
"id": "b5e80b92-bfe4-4667-89bf-88638f4c8bd7",
"type": "gene",
"text": [
"CD14"
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25,
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{
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],
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411,
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]
],
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]
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{
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]
}
] | [] | [] | [] |
88 | 15122513 | [
{
"id": "a4e46286-78f2-40dd-b1d2-4fad449ca942",
"type": "title",
"text": [
"Fibroblast growth factor 20 polymorphisms and haplotypes strongly influence risk of Parkinson disease."
],
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[
0,
103
]
]
},
{
"id": "374534de-fc5c-4de1-a98e-8f546fc66bab",
"type": "abstract",
"text": [
"The pathogenic process responsible for the loss of dopaminergic neurons within the substantia nigra of patients with Parkinson disease (PD) is poorly understood. Current research supports the involvement of fibroblast growth factor ( FGF20 ) in the survival of dopaminergic cells. FGF20 is a neurotrophic factor that is preferentially expressed within the substantia nigra of rat brain. The human homologue has been mapped to 8p21.3-8p22, which is within an area of PD linkage revealed through our published genomic screen. To test whether FGF20 influences risk of PD, we genotyped five single-nucleotide polymorphisms (SNPs) lying within the FGF20 gene, in a large family study. We analyzed our sample (644 families) through use of the pedigree disequilibrium test (PDT), the genotype PDT, the multilocus-genotype PDT, and the family-based association test to assess association between risk of PD and alleles, genotypes, multilocus genotypes, and haplotypes. We discovered a highly significant association of PD with one intronic SNP, rs1989754 (P=.0006), and two SNPs, rs1721100 (P=.02) and ss20399075 (P=.0008), located in the 3' regulatory region in our overall sample. Furthermore, we detected a haplotype (A-G-C-C-T) that is positively associated with risk of PD (P=.0003), whereas a second haplotype (A-G-G-G-C) was found to be negatively associated with risk of PD (P=.0009). Our results strongly support FGF20 as a risk factor for PD."
],
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104,
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]
}
] | [
{
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]
}
] | [] | [] | [] |
89 | 15123570 | [
{
"id": "b7c82267-7e35-4255-bf1c-bdcec2015603",
"type": "title",
"text": [
"Hypoadiponectinemia is an independent risk factor for hypertension."
],
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[
0,
67
]
]
},
{
"id": "7ec6cc3a-8e5e-4bc2-b1c6-2383a1ac0d11",
"type": "abstract",
"text": [
"Adiponectin is one of the key molecules in the metabolic syndrome, and its concentration is decreased in obesity, type-2 diabetes, and coronary artery disease. Genetic investigation has revealed that 2 polymorphisms ( I164T and G276T ) are related to adiponectin concentration and diabetes. To examine whether adiponectin affects hypertension genetically or biologically, we performed a case-control study. A total of 446 diagnosed cases of hypertension (HT) in men and 312 normotensive (NT) men were enrolled in this study. Plasma adiponectin concentration was measured using an enzyme-linked immunosorbent assay system. Single nucleotide polymorphisms were determined by TaqMan polymerase chain reaction method. After adjustment for confounding factors, adiponectin concentration was significantly lower in HT (HT: 5.2+/-0.2 microg/mL; NT: 6.1+/-0.2 microg/mL; P<0.001). Furthermore, multiple regression analysis indicated that hypoadiponectinemia was an independent risk factor for hypertension (P<0.001). Blood pressure was inversely associated with adiponectin concentration in normotensives regardless of insulin resistance. In subjects carrying the TC genotype of the I164T polymorphism, adiponectin concentration was significantly lower (TC: 2.6+/-0.9 microg/mL; TT: 5.5+/-0.1 microg/mL; P<0.01), and most of them had hypertension. In contrast, the G276T polymorphism was not associated with adiponectin concentration or hypertension. In conclusion, hypoadiponectinemia is a marker for predisposition to hypertension in men."
],
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68,
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]
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] | [
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},
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287,
292
]
],
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]
},
{
"id": "fea635ad-8d78-42b9-98bd-dddbd3e827b9",
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299,
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],
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]
},
{
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287,
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],
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{
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299,
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],
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]
}
] | [] | [] | [] |
90 | 15123654 | [
{
"id": "68e07f8a-7ace-499f-b1e3-dde33f063c00",
"type": "title",
"text": [
"Single nucleotide polymorphism ( -468 Gly to A ) at the promoter region of SREBP-1c associates with genetic defect of fructose-induced hepatic lipogenesis [corrected]."
],
"offsets": [
[
0,
169
]
]
},
{
"id": "db919dbc-5fdd-4026-96da-fe4e0793aab3",
"type": "abstract",
"text": [
"To evaluate the genetic susceptibility to metabolic disorders induced by high fructose diet, we investigated the metabolic characteristics in 10 strains of inbred mice and found that they were separated into CBA and DBA groups according to the response to high fructose diet. The hepatic mRNA expression of the sterol regulatory element-binding protein-1 (SREBP-1) in CBA/JN was remarkably enhanced by high fructose diet but not in DBA/2N. Similar results were observed in primary hepatocytes after exposure to fructose. The nucleotide sequence at -468 bp from the putative starting point of the SREBP-1c gene was adenine in the DBA group while it was guanine in the CBA group. In hepatocytes from CBA/JN, the activity of CBA- SREBP-1c promoter was significantly increased by 2.4- and 2.2-fold, in response to 30 mm fructose or 10 nm insulin, respectively, whereas the activity of DBA- SREBP-1c promoter responded to insulin but not to fructose. In hepatocytes from DBA/2N, both types of SREBP-1c promoter activities in response to insulin were attenuated. Furthermore, electrophoretic mobility shift assay revealed an unidentified nuclear protein bound to the oligonucleotides made from the region between -453 to -480 bp of the SREBP-1c promoter of CBA/JN but not to the probe from DBA/2N. Thus, in DBA/2N, the reduced mRNA expression of SREBP-1 after fructose refeeding appeared to associate with two independent mechanisms, 1). loss of binding of unidentified proteins to the region between -453 to -480 bp of the SREBP-1c promoter and 2). impaired insulin stimulation of SREBP-1c promoter activity."
],
"offsets": [
[
170,
1791
]
]
}
] | [
{
"id": "3e6070d7-07a7-47ad-a1c2-2b2bb23827c0",
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],
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482,
535
]
],
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]
},
{
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"SREBP-1c"
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76,
84
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],
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]
},
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"id": "7cbaf682-b1ff-4943-b5b7-b5bfe2d19d4e",
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"SREBP-1c"
],
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76,
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]
],
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]
},
{
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"SREBP-1c"
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76,
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],
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]
},
{
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],
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76,
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],
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},
{
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],
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},
{
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],
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},
{
"id": "95c2c188-e9cd-4ec3-93b9-9ee678486323",
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"text": [
"-468 Gly to A"
],
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33,
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],
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{
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}
]
}
] | [] | [] | [] |
91 | 15124004 | [
{
"id": "b4f80653-bc09-422b-89cc-6ac4ffe55592",
"type": "title",
"text": [
"Variants in the catechol-o-methyltransferase ( COMT ) gene are associated with schizophrenia in Irish high-density families."
],
"offsets": [
[
0,
126
]
]
},
{
"id": "efe5f315-698a-4b31-9ebc-2f113f2a0964",
"type": "abstract",
"text": [
"The enzyme catechol-o-methyltransferase ( COMT ) transfers a methyl group from adenosylmethionine to catecholamines including the neurotransmitters dopamine, epinephrine and norepinephrine. This methylation results in the degradation of catecholamines. The involvement of the COMT gene in the metabolic pathway of these neurotransmitters has made it an attractive candidate gene for many psychiatric disorders. In this article, we reported our study of association of COMT with schizophrenia in Irish families with a high density of schizophrenia. Three single nucleotide polymorphisms (SNPs) were genotyped for the 274 such families and within-family transmission disequilibrium tests were performed. SNP rs4680 , which is the functional Val/Met polymorphism, showed modest association with the disease by the TRANSMIT, FBAT and PDT programs, while the other two SNPs were negative. These SNPs showed lower level of LDs with each other in the Irish subjects than in Ashkenazi Jews. Haplotype analysis indicated that a haplotype, haplotype A-G-A for SNPs rs737865 - rs4680 - rs165599 , was preferentially transmitted to the affected subjects. This was different from the reported G-G-G haplotype found in Ashkenazi Jews, but both haplotypes shared the Val allele. We concluded that COMT gene is associated with schizophrenia and carries a small but significant risk to the susceptibility in the Irish subjects."
],
"offsets": [
[
127,
1547
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]
}
] | [
{
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],
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17,
45
]
],
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}
]
},
{
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"COMT"
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49,
53
]
],
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{
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49,
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},
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49,
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840,
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},
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1190,
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{
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},
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"normalized": [
{
"db_name": "dbSNP",
"db_id": "165599"
}
]
}
] | [] | [] | [] |
92 | 15126335 | [
{
"id": "787d4ee2-5392-467a-b29f-4c0ede068ecb",
"type": "title",
"text": [
"Polymorphisms in DNA double-strand break repair genes and skin cancer risk."
],
"offsets": [
[
0,
75
]
]
},
{
"id": "7d887035-7a41-4f37-9331-3a20dfd8a3b2",
"type": "abstract",
"text": [
"UV can cause a wide range of DNA lesions. UVA-induced oxidative DNA damage and blocked DNA replication by UVB-induced photoproducts can lead to double-strand breaks (DSBs). We selected 11 haplotype-tagging single nucleotide polymorphisms in three DSB repair genes XRCC2 , XRCC3 , and LigaseIV and evaluated their associations with skin cancer risk in a nested case-control study within the Nurses' Health Study [219 melanoma, 286 squamous cell carcinoma (SCC), 300 basal cell carcinoma (BCC), and 873 controls]. We observed that the XRCC3 18085T (241Met) allele and its associated haplotype were significantly inversely associated with the risks of SCC and BCC, whereas the XRCC3 4552C allele along with its associated haplotype and the XRCC2 30833A allele were significantly associated with increased BCC risk. The LigaseIV 4044T and 4062T alleles were associated with decreased BCC risk; two of four haplotypes were significantly associated with altered BCC risk. A trend toward decreased risk of nonmelanoma skin cancer was found in those harboring a greater number of putative low risk alleles (P for trend, 0.05 for SCC, <0.0001 for BCC). The main effects of these genotypes were essentially null for melanoma risk. This study provides evidence to suggest the role of the DSB repair pathway in skin cancer development, especially for BCC."
],
"offsets": [
[
76,
1440
]
]
}
] | [
{
"id": "684c1c7a-29c9-4076-9dd7-882b38bb9851",
"type": "gene",
"text": [
"XRCC2"
],
"offsets": [
[
341,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7516"
}
]
},
{
"id": "98c3c8d2-b4c6-4c09-a6be-b30edd69565e",
"type": "gene",
"text": [
"XRCC3"
],
"offsets": [
[
350,
355
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7517"
}
]
},
{
"id": "9297a9c9-9197-4070-b73e-5212b1e3e945",
"type": "gene",
"text": [
"LigaseIV"
],
"offsets": [
[
363,
371
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "397b0855-ba10-4631-a175-9a95fe8244d6",
"type": "gene",
"text": [
"XRCC3"
],
"offsets": [
[
350,
355
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7517"
}
]
},
{
"id": "3b28c7aa-1bcc-4cad-b3d1-e9fb7d8aa029",
"type": "gene",
"text": [
"XRCC3"
],
"offsets": [
[
350,
355
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7517"
}
]
},
{
"id": "31e9fd1e-78de-4af9-ac89-b8e28d59c67f",
"type": "gene",
"text": [
"XRCC2 "
],
"offsets": [
[
341,
347
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7516"
}
]
},
{
"id": "dbfedcfa-c7c6-4da9-9cee-6141f10ddae5",
"type": "gene",
"text": [
"LigaseIV"
],
"offsets": [
[
363,
371
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "e41bdb93-e8a2-4095-8449-34313e3b51aa",
"type": "variant",
"text": [
"18085T (241Met)"
],
"offsets": [
[
622,
637
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "861539"
}
]
},
{
"id": "9d35f7be-f012-432f-a095-8f4bf7d1dcf2",
"type": "variant",
"text": [
"4552C"
],
"offsets": [
[
767,
772
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "4552C"
}
]
},
{
"id": "0d96f77f-68f7-487d-800e-610070aad2ff",
"type": "variant",
"text": [
"30833A"
],
"offsets": [
[
833,
839
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "30833A"
}
]
},
{
"id": "0c34ca61-57a3-48f0-ba37-bf1df0a098f4",
"type": "variant",
"text": [
"4044T"
],
"offsets": [
[
919,
924
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "4044T"
}
]
},
{
"id": "48e58e62-ad4a-42b7-bbc1-2cb1ed180fa3",
"type": "variant",
"text": [
"4062T"
],
"offsets": [
[
931,
936
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "4062T"
}
]
}
] | [] | [] | [] |
93 | 15129369 | [
{
"id": "265d566b-681b-468e-8c45-0873e56e9f73",
"type": "title",
"text": [
"Two single nucleotide polymorphisms in the CYP17 and COMT Genes--relation to bone mass and longitudinal bone changes in postmenopausal women with or without hormone replacement therapy. The Danish Osteoporosis Prevention Study."
],
"offsets": [
[
0,
231
]
]
},
{
"id": "25a704bc-2489-4c93-bd3e-01414934e06d",
"type": "abstract",
"text": [
"Sex steroids are important physiologic regulators of bone mass, and genes regulating sex steroid production and metabolism are obvious as candidate genes for osteoporosis susceptibility. We present data from a study of 1795 recent postmenopausal women, assigned to either hormone replacement therapy (HRT) or no treatment and followed for 5 years. The association between bone mass measurements and two single nucleotide polymorphisms, a T (A1) to C (A2) transition in the 5'-UTR of the cytochrome P450c17alpha (CYP17) gene and a G (Val) to A (Met) transition in exon 4 of the catechol- O-methyltransferase (COMT) gene, was evaluated. Association with CYP17 genotype was modified by body mass index (BMI). In lean women, individuals homozygous for the CYP17 A2 allele were 1 cm shorter and had lower baseline BMD (bone mineral density), BMC, and CSA (cross sectional area) in the spine and femoral neck than did other women (BMD spine A2A2: 0.975 g/cm2 versus 1.011 g/cm2 in A1A1 + A1A2, P = 0.002). Conversely, an adverse association with A2A2 and bone loss over 5 years seemed present only in overweight women, but differences were small. Response to HRT was not dependent on CYP17 genotype. COMT genotype was not associated with bone mass at baseline, bone loss in untreated women, or response to HRT. In conclusion, the A2 allele of the CYP17 T(27)-C polymorphism is associated with reduced bone mass and bone size in lean perimenopausal women, whereas high BMI protects against this negative association. The COMT G(1947)-A polymorphism is not associated with bone parameters in this study."
],
"offsets": [
[
232,
1847
]
]
}
] | [
{
"id": "0b5f8bc2-7663-4cf5-a164-f57d1d8db46c",
"type": "gene",
"text": [
"CYP17"
],
"offsets": [
[
44,
49
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1586"
}
]
},
{
"id": "772c1c95-2c2a-4e80-bc15-c8347d0fdbcc",
"type": "gene",
"text": [
"CYP17"
],
"offsets": [
[
44,
49
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1586"
}
]
},
{
"id": "b1260a78-0bfc-4a32-89e2-e07ba9385427",
"type": "gene",
"text": [
"CYP17"
],
"offsets": [
[
44,
49
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1586"
}
]
},
{
"id": "d27df5bf-726f-4c7f-bdf0-73c2784d64e4",
"type": "gene",
"text": [
"COMT"
],
"offsets": [
[
56,
60
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1312"
}
]
},
{
"id": "d6c22c9c-5258-4258-852e-08f43c8cc459",
"type": "gene",
"text": [
"CYP17"
],
"offsets": [
[
44,
49
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1586"
}
]
},
{
"id": "9e9901f4-cae8-4666-9b86-1620b8670f27",
"type": "gene",
"text": [
"COMT"
],
"offsets": [
[
56,
60
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1312"
}
]
},
{
"id": "7fe69e68-7b79-4327-8a1f-5969ffc37e38",
"type": "variant",
"text": [
"T (A1) to C (A2) transition in the 5'-UTR of the cytochrome P450c17alpha (CYP17)"
],
"offsets": [
[
671,
751
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "ee80eaf7-af9e-485e-b118-406e734a0b41",
"type": "variant",
"text": [
"G (Val) to A (Met) transition in exon 4 of the catechol- O-methyltransferase (COMT)"
],
"offsets": [
[
765,
848
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "2f052f67-2058-410d-90b5-0609c5d7c5de",
"type": "variant",
"text": [
"T(27)-C"
],
"offsets": [
[
1594,
1601
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T27C"
}
]
},
{
"id": "78eed7fc-9995-480a-b0e8-cd0050d658c9",
"type": "variant",
"text": [
"G(1947)-A"
],
"offsets": [
[
1770,
1779
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G1947A"
}
]
}
] | [] | [] | [] |
94 | 15130757 | [
{
"id": "0b98c6d6-847d-42bb-899a-d01925b92066",
"type": "title",
"text": [
"Modest implication of interleukin-6 promoter polymorphisms in longevity."
],
"offsets": [
[
0,
74
]
]
},
{
"id": "30edf259-3bea-4336-9570-bc9789e892a5",
"type": "abstract",
"text": [
"The multifunctional interleukin-6 has been suggested to contribute to a chronic low-grade inflammatory status, thereby conferring susceptibility to age-related pathological conditions as well as functional decline and increased mortality. Several polymorphisms have been identified in the interleukin-6 promoter, but investigation of the effect of these on interleukin-6 levels and disease susceptibility have led to contradictory results. This study investigates the significance of the three single-point polymorphisms ( -597G/A , -572G/C and -174G/C ) and the AT-stretch polymorphism ( -373(A)n(T)m ) in ageing, by comparison of the frequency of each single polymorphism separately as well as the entire promoter haplotype in a total of 1710 Danish subjects ranging in age from 47 to 100 years. We found a modest, but significant, increase in the frequency of interleukin-6 -174GG homozygotes with age suggesting that this genotype is advantageous for longevity."
],
"offsets": [
[
75,
1053
]
]
}
] | [
{
"id": "eec88dbc-25d0-46fc-87f7-5eac1867d6f3",
"type": "gene",
"text": [
"interleukin-6"
],
"offsets": [
[
23,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3569"
}
]
},
{
"id": "ec9dc7f9-d1bd-448d-a995-a66945deb0cd",
"type": "gene",
"text": [
"interleukin-6"
],
"offsets": [
[
23,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3569"
}
]
},
{
"id": "73c3e70b-64c0-49db-9bf0-15d21db587e9",
"type": "gene",
"text": [
"interleukin-6"
],
"offsets": [
[
23,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3569"
}
]
},
{
"id": "c8fe94a8-6875-4052-84d8-462c75b99fc1",
"type": "gene",
"text": [
"interleukin-6"
],
"offsets": [
[
23,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3569"
}
]
},
{
"id": "81f836f0-2f4a-483a-b0c5-80f07f2d9aa6",
"type": "variant",
"text": [
"-597G/A"
],
"offsets": [
[
604,
611
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-597A"
}
]
},
{
"id": "0d26eaff-36db-4b21-a559-aa2f9085d05f",
"type": "variant",
"text": [
"-572G/C"
],
"offsets": [
[
615,
622
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-572C"
}
]
},
{
"id": "42578e8c-f55f-4932-a158-f0b38bf02da1",
"type": "variant",
"text": [
"-174G/C"
],
"offsets": [
[
629,
636
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-174C"
}
]
},
{
"id": "88cc4596-2107-4951-84c5-fcca632e0446",
"type": "variant",
"text": [
"-373(A)n(T)m"
],
"offsets": [
[
673,
685
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "729fa8cf-930e-46af-bb28-0ac020e4e2f2",
"type": "variant",
"text": [
"-174GG"
],
"offsets": [
[
964,
970
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-174G"
}
]
}
] | [] | [] | [] |
95 | 15138193 | [
{
"id": "9a7fc193-e296-4778-baf1-cc37922b3f1f",
"type": "title",
"text": [
"Toll-like receptor 2 Arg677Trp polymorphism is associated with susceptibility to tuberculosis in Tunisian patients."
],
"offsets": [
[
0,
116
]
]
},
{
"id": "e82af0c8-a9cb-46df-9a6f-7f3a2c90bd9e",
"type": "abstract",
"text": [
"Toll-like receptor 2 (TLR2) is critical in the immune response to mycobacteria. Herein, we report that the frequency of a human TLR2 Arg677Trp polymorphism (C2029T nucleotide substitution) in tuberculosis patients in Tunisia is significantly higher than in healthy controls (P < 0.0001). This finding suggests that this polymorphism could be a risk factor for tuberculosis."
],
"offsets": [
[
117,
495
]
]
}
] | [
{
"id": "95e51448-d8a5-4a3b-94b9-0520cd37e3d3",
"type": "gene",
"text": [
"Toll-like receptor 2 (TLR2)"
],
"offsets": [
[
117,
144
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7097"
}
]
},
{
"id": "3d7f9ea0-1b39-4dda-b987-c5b71f6321e7",
"type": "variant",
"text": [
"Arg677Trp"
],
"offsets": [
[
21,
30
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "R677W"
}
]
},
{
"id": "bd81d045-0fc7-45e0-9d79-6c4205983c8a",
"type": "variant",
"text": [
"(C2029T nucleotide substitution)"
],
"offsets": [
[
277,
309
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C2029T"
}
]
}
] | [] | [] | [] |
96 | 15138458 | [
{
"id": "4cba6e0d-a435-456e-831d-0f75ae7c46b1",
"type": "title",
"text": [
"Evidence for CTLA4 as a susceptibility gene for systemic lupus erythematosus."
],
"offsets": [
[
0,
79
]
]
},
{
"id": "eb098d44-2653-41e8-9fb9-1ad5afe6927e",
"type": "abstract",
"text": [
"Several lines of evidence implicate the Cytotoxic T Lymphocyte Antigen 4 ( CTLA4 ) gene in susceptibility to autoimmune disease. We have examined the association of systemic lupus erythematosus (SLE) with polymorhisms within the CTLA4 gene that were previously proposed to regulate CTLA-4 function: a single nucleotide polymorphism (SNP) in position +49 of exon 1 and a dinucleotide repeat in the 3' untranslated region (3'UTR). The 3'UTR repeat showed a significant association with SLE, with one allele conferring susceptibility and another conferring protection to the disease. The associated alleles do not support previous suggestions of an allele size-dependent effect of the 3' UTR polymorphism in autoimmunity development and instead suggest that it is in linkage disequilibrium with a true causative locus. No association of the exon 1 SNP with SLE was found in our population. Given the conflicting results obtained in different studies on the association of SLE with this polymorphism, we performed a meta-analysis including seven previously published studies and the present one. Significantly increased and decreased risks for SLE were found for carriers of the G allele and the A allele, respectively. The functional characterization of disease-associated CTLA4 gene variants is now required to elucidate their role in the pathogenesis of SLE and other autoimmune diseases."
],
"offsets": [
[
80,
1477
]
]
}
] | [
{
"id": "2e5bfb20-101d-441e-a3d4-637021e0fd11",
"type": "gene",
"text": [
"Cytotoxic T Lymphocyte Antigen 4"
],
"offsets": [
[
121,
153
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "149fe168-97f8-4d5f-a48f-6e7f5f41f6e7",
"type": "gene",
"text": [
"CTLA4"
],
"offsets": [
[
14,
19
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "6a77c875-59c0-4a10-9a7a-28f094b378c4",
"type": "gene",
"text": [
"CTLA4"
],
"offsets": [
[
14,
19
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "17e73efe-0d7a-4b29-8bc3-88589bafed4d",
"type": "gene",
"text": [
"CTLA-4"
],
"offsets": [
[
367,
373
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "2311e484-d430-43ab-92a0-52c49d62ee85",
"type": "gene",
"text": [
"CTLA4"
],
"offsets": [
[
14,
19
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "2b7d6de2-8921-4f20-b55c-3f427ad4ebf6",
"type": "variant",
"text": [
"single nucleotide polymorphism (SNP) in position +49 of exon 1"
],
"offsets": [
[
388,
450
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
}
] | [] | [] | [] |
97 | 15138483 | [
{
"id": "4151fc43-4186-4c8d-8ed6-d1c8400e28dd",
"type": "title",
"text": [
"Association of NQO1 polymorphism with spontaneous breast cancer in two independent populations."
],
"offsets": [
[
0,
97
]
]
},
{
"id": "c738b86a-b86b-4767-94b3-a67b71ddd815",
"type": "abstract",
"text": [
"Eight different single-nucleotide polymorphisms (SNPs) in six different genes were investigated for possible association with breast cancer. We used a case-control study design in two Caucasian populations, one from Tyrol, Austria, and the other from Prague, Czech Republic. Two SNPs showed an association with breast cancer: R72P in TP53 and P187S in NQO1 . Six SNPs, Q356R and P871L in BRCA1 , N372H in BRCA2 , C112R (E4) and R158C (E2) in ApoE and C825T in GNB3 , did not show any sign of association. The P187S polymorphism in NQO1 was associated with breast cancer in both populations from Tyrol and Prague with a higher risk for carriers of the 187S allele. Combining the results of the two populations, we observed a highly significant difference (P=0.0004) of genotype and allele frequencies (odds ratio (OR)=1.46; 95% confidence interval (CI) 1.16-1.85; P=0.001) and of the homozygote ratio (OR=3.8; 95% CI 1.73-8.34; P=0.0001). Combining the two 'candidate' SNPs ( P187S and R72P ) revealed an increased risk for breast cancer of double heterozygotes ( P187S / R72P ) of the NQO1 and TP53 genes (OR=1.88; 95% CI 1.13-3.15; P=0.011), suggesting a possible interaction of these two loci."
],
"offsets": [
[
98,
1328
]
]
}
] | [
{
"id": "ad189f4d-ff1d-4103-94d7-b4cc3c85c9f7",
"type": "gene",
"text": [
"TP53"
],
"offsets": [
[
434,
438
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "d13ce59d-53ab-43bb-906c-6224095376f2",
"type": "gene",
"text": [
"NQO1"
],
"offsets": [
[
16,
20
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1728"
}
]
},
{
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]
}
] | [] | [] | [] |
98 | 15138485 | [
{
"id": "29948e84-4604-4bf0-a480-6b84d4270120",
"type": "title",
"text": [
"A single-nucleotide polymorphism in the RAD51 gene modifies breast cancer risk in BRCA2 carriers, but not in BRCA1 carriers or noncarriers."
],
"offsets": [
[
0,
145
]
]
},
{
"id": "09c97269-a8d5-4c7e-847a-7569a9a0e97a",
"type": "abstract",
"text": [
"Variation in the penetrance estimates for BRCA1 and BRCA2 mutation carriers suggests that other genetic polymorphisms may modify the cancer risk in carriers. The RAD51 gene, which participates in homologous recombination double-strand breaks (DSB) repair in the same pathway as the BRCA1 and BRCA2 gene products, is a candidate for such an effect. A single-nucleotide polymorphism (SNP), RAD51-135g-->c , in the 5' untranslated region of the gene has been found to elevate breast cancer (BC) risk among BRCA2 carriers. We genotyped 309 BRCA1 /2 mutation carriers, of which 280 were of Ashkenazi origin, 166 noncarrier BC patients and 152 women unaffected with BC (a control group), for the RAD51-135g-->c SNP. Risk analyses were conducted using COX proportional hazard models for the BRCA1 /2 carriers and simple logistic regression analysis for the noncarrier case-control population. BRCA2 carriers were also studied using logistic regression and Kaplan-Meier survival analyses. The estimated BC hazard ratio (HR) for RAD51-135c carriers adjusted for origin (Ashkenazi vs non-Ashkenazi) was 1.28 (95% CI 0.85-1.90, P=0.23) for BRCA1 /2 carriers, and 2.09 (95% CI 1.04-4.18, P=0.04) when the analysis was restricted to BRCA2 carriers. The median BC age was younger in BRCA2 - RAD51-135c carriers (45 (95% CI 36-54) vs 52 years (95% CI 48-56), P=0.05). In a logistic regression analysis, the odds ratio (OR) was 5.49 (95% CI 0.5-58.8, P=0.163). In noncarrier BC cases, carrying RAD51-135c was not associated with BC risk (0.97; 95% CI 0.47-2.00). These results indicate significantly elevated risk for BC in carriers of BRCA2 mutations who also carry a RAD51-135c allele. In BRCA1 carriers and noncarriers, no effect for this SNP was found."
],
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[
146,
1920
]
]
}
] | [
{
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"BRCA1"
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114,
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]
],
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}
]
},
{
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85,
90
]
],
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]
},
{
"id": "d56920c8-d38c-4a82-a5bc-cbd5d5d02144",
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"text": [
"RAD51"
],
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41,
46
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],
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]
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{
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"BRCA1"
],
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114,
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]
],
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}
]
},
{
"id": "eaea7679-ff55-4bf2-8a87-ab0c57c3eb64",
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"BRCA2"
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85,
90
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],
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]
},
{
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"BRCA2"
],
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85,
90
]
],
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}
]
},
{
"id": "11754cab-156d-46bc-8f15-d7c629060f3c",
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"BRCA1"
],
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114,
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],
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]
},
{
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"BRCA1"
],
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]
},
{
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"BRCA2"
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{
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]
},
{
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"BRCA2"
],
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]
},
{
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"BRCA2"
],
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85,
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]
],
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"db_id": "675"
}
]
},
{
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"BRCA2"
],
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],
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]
},
{
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],
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114,
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]
],
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}
]
},
{
"id": "11b6a259-dfbe-476b-b71e-07393358a65e",
"type": "variant",
"text": [
"RAD51-135g-->c"
],
"offsets": [
[
545,
559
]
],
"normalized": [
{
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"db_id": "G135C"
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]
},
{
"id": "8498f28e-a964-432b-ad8e-2c067a8846ab",
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"text": [
"RAD51-135g-->c"
],
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[
545,
559
]
],
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"db_id": "G135C"
}
]
},
{
"id": "6023b4af-c04a-4249-becb-08aa992c87f0",
"type": "variant",
"text": [
"RAD51-135c"
],
"offsets": [
[
1186,
1196
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "135C"
}
]
},
{
"id": "0c867328-9761-44ab-8185-07cca00d390f",
"type": "variant",
"text": [
"RAD51-135c"
],
"offsets": [
[
1186,
1196
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "135C"
}
]
},
{
"id": "ec97aaf1-3f01-4858-b3e3-2aebc0463582",
"type": "variant",
"text": [
"RAD51-135c"
],
"offsets": [
[
1186,
1196
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "135C"
}
]
},
{
"id": "4425f175-b31d-4269-a87c-de912e1efaf4",
"type": "variant",
"text": [
"RAD51-135c"
],
"offsets": [
[
1186,
1196
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "135C"
}
]
}
] | [] | [] | [] |
99 | 15142217 | [
{
"id": "ef155cca-393b-4d7b-b0a1-a2f2a641f245",
"type": "title",
"text": [
"Association of tumor necrosis factor receptor type 2 +587 gene polymorphism with severe chronic periodontitis."
],
"offsets": [
[
0,
112
]
]
},
{
"id": "1f4ee53d-22fa-4c7f-b12c-3c493ef0d5ea",
"type": "abstract",
"text": [
"BACKGROUND: Genetic polymorphisms for cytokines and their receptors have been proposed as potential markers for periodontal disease. Tumor necrosis factor receptor 2 ( TNFR2 ) is one of the cell surface receptors for TNF-alpha . Recent studies have suggested that TNFR2 gene polymorphism is involved in autoimmune and other diseases. OBJECTIVES: The aim of the present study is to evaluate whether TNFR2 ( +587T/G ) gene polymorphism is associated with chronic periodontitis (CP). METHODS: One hundred and ninety-six unrelated subjects (age 40-65 years) with different levels of CP were identified according to established criteria, including measurements of probing pocket depth (PPD), clinical attachment level (CAL), and alveolar bone loss (BL). All subjects were of Japanese descent and non-smokers. Single nucleotide polymorphism at position +587(T/G) in the TNFR2 gene was detected by a polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) method. RESULTS: The frequency and the positivity of the +587G allele were significantly higher in severe CP patients than in controls (p=0.0097; odds ratio=2.61, p=0.0075; odds ratio=3.06). In addition, mean values of PPD, CAL, and BL were significantly higher in the +587G allele positive than in the negative subjects (p=0.035, 0.022, and 0.018, respectively). CONCLUSIONS: These findings suggest that the TNFR2 ( +587G ) polymorphic allele could be associated with severe CP in Japanese."
],
"offsets": [
[
113,
1591
]
]
}
] | [
{
"id": "e0f9838e-bb6f-4871-80b3-1a036cd02b3c",
"type": "gene",
"text": [
"Tumor necrosis factor receptor 2"
],
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[
247,
279
]
],
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]
},
{
"id": "e11869e2-fccd-4a28-8c8b-21d49691009b",
"type": "gene",
"text": [
"TNFR2"
],
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283,
288
]
],
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]
},
{
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"type": "gene",
"text": [
"TNF-alpha"
],
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333,
342
]
],
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]
},
{
"id": "f24a86cb-3c56-4f21-b47a-308b12a0ec11",
"type": "gene",
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"TNFR2"
],
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283,
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]
],
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}
]
},
{
"id": "68d311f1-4ec3-4c43-9723-8460fffacc67",
"type": "gene",
"text": [
"TNFR2"
],
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[
283,
288
]
],
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]
},
{
"id": "bdf5f2d4-b289-4c9d-af42-3717af4055ce",
"type": "gene",
"text": [
"TNFR2"
],
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[
283,
288
]
],
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}
]
},
{
"id": "fde83ac8-4dac-421c-bd08-087fd1fa977b",
"type": "gene",
"text": [
"TNFR2"
],
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[
283,
288
]
],
"normalized": [
{
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"db_id": "7133"
}
]
},
{
"id": "4cb318cb-327a-4b1d-80f3-784b5d216c28",
"type": "variant",
"text": [
"+587T/G"
],
"offsets": [
[
525,
532
]
],
"normalized": [
{
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"db_id": "1061622"
}
]
},
{
"id": "7e61eeb3-3b91-4ab3-a3f4-572c7f914e4c",
"type": "variant",
"text": [
"+587(T/G)"
],
"offsets": [
[
967,
976
]
],
"normalized": [
{
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"db_id": "1061622"
}
]
},
{
"id": "4e422cef-4a64-4992-a46e-5494dae6a935",
"type": "variant",
"text": [
"+587G"
],
"offsets": [
[
1153,
1158
]
],
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}
]
},
{
"id": "5e6d6296-8430-49c3-afa8-2557ad570af5",
"type": "variant",
"text": [
"+587G"
],
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[
1153,
1158
]
],
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"db_id": "1061622"
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]
},
{
"id": "7b97ee86-49f8-4cd7-b58e-31fdd641e5a5",
"type": "variant",
"text": [
"+587G"
],
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[
1153,
1158
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1061622"
}
]
}
] | [] | [] | [] |
100 | 15149891 | [
{
"id": "1c104869-89e5-4bfb-a853-7f07396bc8a8",
"type": "title",
"text": [
"Simple and rapid detection of uncoupling protein-2 - 866G/A polymorphism by mutagenically separated polymerase chain reaction."
],
"offsets": [
[
0,
130
]
]
},
{
"id": "b891cab4-58e8-442f-a9cf-ce5ee506defe",
"type": "abstract",
"text": [
"BACKGROUND: Uncoupling protein-2 ( UCP2 ), a recently identified member of the mitochondrial transporter superfamily, is a candidate gene for obesity. A common G/A polymorphism in the UCP2 promoter region is associated with enhanced adipose tissue mRNA expression in vivo. METHODS: We developed a rapid and simple method, mutagenically separated polymerase chain reaction (MS-PCR) for genotyping UCP2 - 866G/A polymorphism. Two reverse mutagenic allele-specific primers of different lengths for the UCP2 - 866G/A polymorphic site were paired with the same forward primer in the same PCR reaction. RESULTS: Agarose gel electrophoresis (3.5%) showed at least one of the two allelic products and provided a within-assay quality control to exclude false-negative results. The 203-bp fragment of the PCR products was A allele-specific and the 183-bp fragment was G allele-specific. The frequencies of the UCP2 - 866G/A genotypes in 72 Japanese subjects were AA: 21 (29.2%), AG: 32 (44.4%), and GG: 19 (26.4%). The results were confirmed by the PCR-RFLP genotyping method, in which a 360-bp fragment of PCR products was cut into 290- and 70-bp fragments by the restriction enzyme MluI when the G allele was present. This Japanese group showed a higher frequency of the AA genotype, which is associated with a low prevalence of obesity, than Caucasian populations. CONCLUSIONS: The MS-PCR technique is a simple, rapid, and reliable method for genotyping UCP2 - 866G/A polymorphism."
],
"offsets": [
[
131,
1625
]
]
}
] | [
{
"id": "7380406b-7993-442f-8135-047086162993",
"type": "gene",
"text": [
"Uncoupling protein-2"
],
"offsets": [
[
144,
164
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "d5da9bb4-5484-4699-8bbe-f9cf55990237",
"type": "gene",
"text": [
"UCP2"
],
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168,
172
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "465ce9bb-95d3-44e4-916f-647f616ef580",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
168,
172
]
],
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{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "db2cb5d8-786d-43da-9408-3dc6f965284e",
"type": "gene",
"text": [
"UCP2"
],
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[
168,
172
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "1d562780-962a-49be-b4c8-2341b1a060ff",
"type": "gene",
"text": [
"UCP2"
],
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[
168,
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]
],
"normalized": [
{
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"db_id": "7351"
}
]
},
{
"id": "fc3b6ee3-dce4-43f5-bea9-7eb02c47ea47",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
168,
172
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "19bc2481-b93c-4ede-bf6a-f81f8b2a768d",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
168,
172
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "2ecf7fd2-df53-4ef3-8f45-13f3344f0a8a",
"type": "variant",
"text": [
"- 866G/A"
],
"offsets": [
[
54,
62
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
},
{
"id": "09049cd7-cc32-41bc-a985-e632033ccaff",
"type": "variant",
"text": [
"- 866G/A"
],
"offsets": [
[
54,
62
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
},
{
"id": "f5e2e349-f410-4671-9347-e85e4d746f72",
"type": "variant",
"text": [
"- 866G/A"
],
"offsets": [
[
54,
62
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
},
{
"id": "281d124a-3007-4ed4-b95f-069ade5fb10f",
"type": "variant",
"text": [
"- 866G/A"
],
"offsets": [
[
54,
62
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
}
] | [] | [] | [] |
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