shlokn/autogkb huggingface dataset:
Article: ADH single nucleotide polymorphism associations with alcohol metabolism in vivo
Gene: ADH1B
Variant/haplotype: rs17033
Drug(s): ethanol
Phenotype category: Toxicity, Metabolism/PK
Significant: yes
Association: Allele C is associated with metabolism of ethanol.
Notes: The authors did not report p-value correction for multiple hypotheses (103 snps tested).  Though they report multiple snps are significantly associated with alcohol metabolism (early or late) tested on blood or breath alcohol concentrations, this snp is NOT significant after Bonferroni correction (<0.00049).  Also, the authors did not state which alleles are associated with increased or decreased metabolism.  Instead, they simply report an association with the snp in general.  Note that this gene is on the minus strand.
Article: Pharmacodynamic and kinetic effect of rabeprazole on serum gastrin level in relation to CYP2C19 polymorphism in Chinese Hans
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): rabeprazole
Phenotype category: Metabolism/PK
Significant: no
Association: CYP2C19 *1/*1 is not associated with metabolism of rabeprazole in healthy individuals as compared to CYP2C19 *1/*2 + *1/*3.
Notes: No significant difference in area under the concentration-time curve (AUC) for rabeprazole were seen between the two genotype groups. Subjects were given rabeprazole for 8 days; AUC was measured on day 1 and day 8 after rabeprazole administration. Please note that the *2 and *3 alleles were referred to by their previous designations (CYP2C19*m1 and *m2, respectively).
Article: Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder
Gene: BMAL1
Variant/haplotype: rs1982350
Drug(s): lithium
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with increased response to lithium in people with Bipolar Disorder as compared to allele G.
Article: Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes
Gene: CYP2A6
Variant/haplotype: rs777098658
Drug(s): nicotine
Phenotype category: Metabolism/PK
Significant: not stated
Association: Allele G is associated with decreased metabolism of nicotine as compared to allele A.
Notes: Assigned as decreased function following in vitro assessments, in vivo associations and variant construct functional assignments.
Article: Impact of CYP2C19 genotype on sertraline exposure in 1200 Scandinavian patients
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): sertraline
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*2 + *1/*3 (assigned as intermediate metabolizer phenotype) are associated with decreased metabolism of sertraline as compared to CYP2C19 *1/*1 (assigned as normal metabolizer phenotype) .
Notes: Compared with the CYP2C19 NMs (*1/*1), the sertraline serum concentration was increased 1.38-fold (p < 0.001, 95% CI 1.26–1.50) in CYP2C19 IMs (carriers of one no function alleles in combination with either *17 or *1). A 1.47-fold (p < 0.001, 95% CI 1.35–1.60)  higher concentration of N-desmethylsertraline was found in IMs. Compared with NMs, the N-desmethylsertraline-to-sertraline metabolic ratio was  1.14-fold higher ratio in IMs (p < 0.001, 95% CI 1.06–1.22). In CYP2C19 IMs, the OR for having one or more TDM measurements above the target concentration range of 250 nM was  1.97 (p = 0.064, CI: 1.21–3.21), compared to CYP2C19 NMs. Study identified *2, *3, and *4 as no function alleles but not reported specific diplotypes, the diplotypes in the annotations are used as a representation.
Article: Pharmacogenomics of Methotrexate Membrane Transport Pathway: Can Clinical Response to Methotrexate in Rheumatoid Arthritis Be Predicted?
Gene: ABCC1
Variant/haplotype: rs246240
Drug(s): methotrexate
Phenotype category: Efficacy
Significant: yes
Association: Genotypes AG + GG are associated with decreased response to methotrexate in people with Arthritis, Rheumatoid as compared to genotype AA.
Notes: ABCC1 rs246240 G carrier is associated with increased risk of non-response to methotrexate.
Article: Pharmacogenetics of tenofovir clearance among Southern Africans living with HIV
Gene: ABCC4
Variant/haplotype: rs1751034
Drug(s): tenofovir
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with clearance of tenofovir in people with HIV Infections as compared to allele C.
Notes: Based on available allele frequency data, it is assumed that the paper compares the C and T alleles.
Article: Effects of CYP3A4 and CYP2C9 genotype on systemic anastrozole and fulvestrant concentrations in SWOG S0226
Gene: CYP2C9
Variant/haplotype: CYP2C9 intermediate metabolizer
Drug(s): anastrozole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C9 intermediate metabolizer and poor metabolizer is associated with decreased concentrations of anastrozole in people with Breast Neoplasms and Neoplasm Metastasis as compared to CYP2C9 normal metabolizer and ultrarapid metabolizer.
Notes: Alleles measured included CYP2C9*2, CYP2C9*3 (or*18), CYP2C9*4, CYP2C9*5, CYP2C9*6, CYP2C9*8, CYP2C9*9, CYP2C9*10, CYP2C9*11, CYP2C9*12, CYP2C9*13, CYP2C9*15, CYP2C9*25 and CYP2C9*27. Alleles and phenotypes were modeled after CPIC. "participants with low CYP2C9 activity had lower anastrozole concentrations and higher fulvestrant concentrations than participants with high CYP2C9 activity"
Article: Identification of two novel genes SLC15A2 and SLCO1B3 associated with maintenance dose variability of warfarin in a Chinese population
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Genotype TT is associated with decreased dose of warfarin as compared to genotype CC.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: DCK
Variant/haplotype: rs4694362
Drug(s): gemcitabine
Phenotype category: Efficacy
Significant: no
Association: Genotype TT is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes CT + TT.
Notes: Tumor response to therapy and progression free survival did not significantly differ between genotype groups.
Article: GENE AND GENE BY SEX ASSOCIATIONS WITH INITIAL SENSITIVITY TO NICOTINE IN NONSMOKERS
Gene: DRD2
Variant/haplotype: rs6277
Drug(s): nicotine
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to nicotine in men as compared to allele G.
Notes: Please note that alleles have been complemented to the positive strand. Male subjects with the AA genotype had a higher perception score of "feel the effects" of nicotine with 5ug/kg nicotine, while male subjects with the AA or AG genotypes had higher "feel the effects" scores with 10ug/kg. Male subjects with the AA genotype had decreased fatigue and increased anger in the mood scoring compared to male subjects with the AG or GG genotypes. There was no significant association between this variant and physiological responses to nicotine, performance task responses or nicotine reinforcement.
Article: NAT2 genotype guided regimen reduces isoniazid-induced liver injury and early treatment failure in the 6-month four-drug standard treatment of tuberculosis: A randomized controlled trial for pharmacogenetics-based therapy
Gene: NAT2
Variant/haplotype: NAT2*4, NAT2*6, NAT2*7, NAT2*14, NAT2*16, NAT2*19
Drug(s): isoniazid
Phenotype category: Dosage, Metabolism/PK
Significant: yes
Association: NAT2 *4/*4 (assigned as rapid acetylator phenotype) is associated with increased dose of isoniazid in people with Tuberculosis as compared to NAT2 *19 + *14 + *16 + *6 + *7 (assigned as slow acetylator phenotype) .
Notes: Originally annotated as "compared to NAT2 *19 + *14A + *5D + *6B + *7A (assigned as slow acetylator phenotype)". Patients were given an isoniazid dose based on NAT2 acetylator status or a standard dose. Slow acetylators (carriers of two variant alleles *19, *14, *5, *6, or *7) who had their dose adjusted had a reduced incidence of liver injury as compared to those who received a standard dose, and fast acetylators (*4/*4,  either given standard dose or 1.5x standard dose) who had their dose adjusted had a reduced incidence of early treatment failure (at 8 weeks) as compared to those who received a standard dose.; The arylamine N-acetyltransferases (NATs) database was transitioned into the PharmVar database in March 2024. the alleles included in this annotation are mapped as following: NAT2*14A under the *14 core allele; NAT2*5D under the *16 core allele; NAT2*6B under the *6 core allele; NAT2*7A under the *7 core allele.
Article: A functional polymorphism in the ABCB1 transporter predicts pharmacologic response to combination of nortriptyline and morphine in neuropathic pain patients
Gene: ABCB1
Variant/haplotype: rs1045642
Drug(s): morphine, nortriptyline
Phenotype category: Efficacy
Significant: yes
Association: Genotype GG is associated with increased response to morphine and nortriptyline in people with Pain as compared to genotypes AA + AG.
Notes: Patients with the GG genotype had a significantly greater improvement in pain scores compared to those with the AA or AG genotypes. Please note that alleles have been complemented to the positive strand.
Article: Association Between Vitamin D Receptor Polymorphism and the Response to Helicobacter Pylori Treatment
Gene: VDR
Variant/haplotype: rs7975232
Drug(s): amoxicillin, clarithromycin, omeprazole
Phenotype category: Efficacy
Significant: yes
Association: Allele A is associated with increased response to amoxicillin, clarithromycin and omeprazole in people with Helicobacter Infections as compared to allele C.
Article: Genome-Wide Association Study of Serum Creatinine Levels during Vancomycin Therapy
Variant/haplotype: rs9293392
Drug(s): vancomycin
Phenotype category: Metabolism/PK
Significant: no
Association: Allele T is not associated with trough concentration of vancomycin as compared to allele C.
Notes: The SNP was not associated with trough levels of vancomycin (first vancomycin trough documented in EMR after at least 3 doses vancomycin). Elimination constants were also calculated.
Article: Gemcitabine Metabolic and Transporter Gene Polymorphisms Are Associated with Drug Toxicity and Efficacy in Patients with Locally Advanced Pancreatic Cancer
Gene: SLC29A1
Variant/haplotype: rs324148
Drug(s): gemcitabine
Phenotype category: Efficacy, Toxicity
Significant: no
Association: Genotype CC is not associated with increased response to gemcitabine in people with Pancreatic Neoplasms as compared to genotypes CT + TT.
Notes: Tumor response to therapy, progression free survival, and risk of neutropenia development did not significantly differ between genotype groups.
Article: Genetic Variation in CYP3A43 Explains Racial Difference in Olanzapine Clearance
Variant/haplotype: rs2859228
Drug(s): olanzapine
Phenotype category: Metabolism/PK
Significant: no
Association: Allele A is not associated with clearance of olanzapine in people with Schizophrenia as compared to allele G.
Article: Human Polymorphisms in the Glutathione Transferase Zeta 1/Maleylacetoacetate Isomerase Gene Influence the Toxicokinetics of Dichloroacetate
Gene: GSTZ1, POMT2
Variant/haplotype: rs7972
Drug(s): dichloroacetic acid
Phenotype category: Other, Metabolism/PK
Significant: yes
Association: Allele G is associated with increased metabolism of dichloroacetic acid in healthy individuals.
Notes: The statement above  is meant for a haplotype rather than for the allele.  For the various possible haplotype combinations involving rs7975,rs7972,rs1046428, the most rapid clearance was observed for subjects having at least one "wild-type" allele (G for rs7975,G for rs7972, C for rs1046428. Rate was 2.2 +/- 0.7 vs 0.73 +/- 0.84 mL/min,  and the very highest rate was seen in homozygous "wild-type".
Article: Genome-Wide Association and Functional Studies Reveal Novel Pharmacological Mechanisms for Allopurinol
Gene: GREM2
Variant/haplotype: rs77567654
Drug(s): allopurinol
Phenotype category: Efficacy
Significant: yes
Association: Allele G is associated with increased response to allopurinol as compared to allele A.
Notes: Response to allopurinol was determined by whether serum uric acid concentrations decreased following allopurinol treatment. This SNP is in strong LD with rs1934341.
Article: A pharmacogenetic pilot study reveals MTHFR, DRD3, and MDR1 polymorphisms as biomarker candidates for slow atorvastatin metabolizers
Gene: SLCO1B1
Variant/haplotype: rs4149056
Drug(s): atorvastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes CC + CT are associated with increased concentrations of atorvastatin in healthy individuals as compared to genotype TT.
Article: Genome-wide association study of patient and clinician rated global impression severity during antipsychotic treatment
Variant/haplotype: rs7395555
Drug(s): risperidone
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased response to risperidone in people with Schizophrenia as compared to allele G.
Notes: The number of C alleles present in a patient was negatively associated with CGI-S score.
Article: A GENOME-WIDE ASSOCIATION STUDY OF BRONCHODILATOR RESPONSE IN LATINOS IMPLICATES RARE VARIANTS
Variant/haplotype: rs116551936
Drug(s): salbutamol
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with increased response to salbutamol in children with Asthma as compared to genotype GG.
Notes: The allele associated with increased response and low frequency is not explicitly stated.  Response is increased for carriers of the rare, minor allele.  GALAII genotyping was done using the Affymetrix LAT1 Array, which was designed to capture Latino population variation.
Article: A Pharmacogenetics-Based Warfarin Maintenance Dosing Algorithm from Northern Chinese Patients
Gene: CYP2C19
Variant/haplotype: rs4986893
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with dose of warfarin in people with heart valve replacement as compared to allele A.
Notes: Samples, genotypes and INRs from a cohort of 551 patients were used to derive an algorithm which was used to predict daily warfarin maintenance dose in a second cohort of 236 patients. Note: the authors state that "SNPs were tested for deviations from HWE using the chi-squared test, and for their association with the warfarin dose by Spearman correlation analysis using a *co-dominant* model."
Article: VKORC1 and Novel CYP2C9 Variation Predict Warfarin Response in Alaska Native and American Indian People
Gene: GGCX
Variant/haplotype: rs11676382
Drug(s): warfarin
Phenotype category: Dosage
Significant: no
Association: Allele G is not associated with decreased dose of warfarin as compared to allele C.
Notes: in Alaska Native and American Indian People.
Article: Influence of FMO3 and CYP3A4 Polymorphisms on the Pharmacokinetics of Teneligliptin in Humans
Gene: FMO3
Variant/haplotype: rs2266782
Drug(s): teneligliptin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotypes AG + GG is associated with decreased clearance of teneligliptin in men as compared to genotype AA.
Notes: effect described for (rs2266780/rs2266782). Significant for clearance, Cmax, and AUC.
Article: Warfarin pharmacogenetics: a single VKORC1 polymorphism is predictive of dose across 3 racial groups
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin as compared to allele C.
Article: Single Nucleotide Variant in Nucleoporin 107 may be Predictive of Sensitivity to Chemotherapy in Patient with Ovarian Cancer
Gene: NUP107
Variant/haplotype: rs79419059
Drug(s): Platinum compounds
Phenotype category: Efficacy
Significant: yes
Association: Allele C is associated with increased resistance to Platinum compounds in women with Ovarian Neoplasms as compared to allele T.
Notes: In the cohort, 25 patients received carboplatin-based first line therapy and 3 received cisplatin therapy. Controlling for other con-founders, multivariate age-adjusted Cox proportional hazard analysis showed that the variant rs79419059  was significantly associated with platinum resistance [odds ratio: 4.519, 95% confidence interval (CI): 1.317–15.501, P = 0.0457].
Article: Genetic factors influencing warfarin dose in Black-African patients: a systematic review and meta-analysis
Gene: CYP2C9
Variant/haplotype: CYP2C9*1, CYP2C9*2
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: CYP2C9 *1/*2 is associated with decreased dose of warfarin as compared to CYP2C9 *1/*1.
Notes: In this meta-analysis of warfarin Dose in Black-African Patients, CYP2C9*2 allele is associated with 6.8mg/week less warfarin dose requirement compared to wild-type homozygotes.
Article: Evaluation of CYP2C9- and VKORC1-based pharmacogenetic algorithm for warfarin dose in Gaza-Palestine
Gene: VKORC1
Variant/haplotype: rs9923231
Drug(s): warfarin
Phenotype category: Dosage
Significant: yes
Association: Allele T is associated with decreased dose of warfarin in people with Cardiovascular Diseases as compared to allele C.
Article: Association of ABCC2 polymorphism with clopidogrel response in Chinese patients undergoing percutaneous coronary intervention
Gene: CYP2C19
Variant/haplotype: rs4986893
Drug(s): clopidogrel
Phenotype category: Efficacy
Significant: yes
Association: Genotype AG is associated with decreased response to clopidogrel in people with Coronary Artery Disease as compared to genotype GG.
Notes: "CYP2C19*3 GA carriers presented significantly lower mean PAIR% values (66.39 ± 25.68) than CYP2C19*3 GG carriers". There were only 3 AA individuals.
Article: Potentially Functional SNPs (pfSNPs) as Novel Genomic Predictors of 5-FU Response in Metastatic Colorectal Cancer Patients
Gene: TK1
Variant/haplotype: rs8071253
Drug(s): capecitabine, fluorouracil
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to capecitabine and fluorouracil in people with Neoplasm Metastasis as compared to allele G.
Article: Secondary metabolism pathway polymorphisms and plasma efavirenz concentrations in HIV-infected adults with CYP2B6 slow metabolizer genotypes
Gene: UGT2B7
Variant/haplotype: rs28365062
Drug(s): efavirenz
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype GG is associated with decreased metabolism of efavirenz in people with HIV Infections as compared to genotypes AA + AG.
Notes: As measured by increased plasma concentrations in patients with the GG genotype compared to the other genotypes (allele model was not statistically significant, perhaps due to low numbers of patients with the GG genotype). *Note: All participants were CYP2B6 slow metabolizers (defined by the following genotypes of two SNPs: rs3745274 TT, or  rs3745274 T/rs28399499 C or rs28399499 CC).*
Article: Evaluation of the Effect of CYP2D6 Genotypes on Tramadol and O-Desmethyltramadol Pharmacokinetic Profiles in a Korean Population Using Physiologically-Based Pharmacokinetic Modeling
Gene: CYP2D6
Variant/haplotype: CYP2D6 poor metabolizers and intermediate metabolizers
Drug(s): o-desmethyltramadol
Phenotype category: Metabolism/PK
Significant: not stated
Association: CYP2D6 intermediate metabolizer and poor metabolizer are associated with decreased concentrations of o-desmethyltramadol in healthy individuals as compared to CYP2D6 normal metabolizer.
Notes: Note that no statistical analysis was carried out on data from the clinical study. All IMs had the *10/*10 genotype, while all PMs had the *5/*5 genotype. The genotypes of all NMs are not given and the study did not look for CNVs to identify UMs.
Article: CALCA and TRPV1 genes polymorphisms are related to a good outcome in female chronic migraine patients treated with OnabotulinumtoxinA
Gene: TRPM8
Variant/haplotype: rs10166942
Drug(s): botulinum toxin type a
Phenotype category: Efficacy
Significant: no
Association: Allele C is not associated with response to botulinum toxin type a in women with Migraine NOS as compared to allele T.
Notes: No significant difference in allele frequency between responders and non-responders.
Article: Pharmacokinetics and response to pravastatin in paediatric patients with familial hypercholesterolaemia and in paediatric cardiac transplant recipients in relation to polymorphisms of the SLCO1B1 and ABCB1 genes
Gene: SLCO1B1
Variant/haplotype: rs4149015
Drug(s): pravastatin
Phenotype category: Metabolism/PK
Significant: yes
Association: Genotype AG is associated with increased metabolism of pravastatin in children with Hyperlipoproteinemia Type II as compared to genotype GG.
Notes: 2 patients with the AG genotype (who also had rs4149056 genotype TC) had significantly lower plasma Cmax and AUC. This variant was described as -11187G>A.
Article: Impact of Gastric H+/K+-ATPase rs2733743 on the Intragastric pH-Values of Dexlansoprazole Injection in Chinese Subjects
Gene: CYP2C19
Variant/haplotype: CYP2C19*1, CYP2C19*2, CYP2C19*3
Drug(s): dexlansoprazole
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP2C19 *1/*2 + *1/*3 are associated with decreased metabolism of dexlansoprazole in healthy individuals as compared to CYP2C19 *1/*1.
Notes: CYP2C19*2 (rs4244285), CYP2C19*3 (rs4986893), CYP2C19*17 (rs12248560) were genotyped but only *2 and *3 were identified. CYP2C19 PMs presented a slower elimination and higher exposure (Cmax and AUCPK) compared to CYP2C19 homEMs, while the elimination and exposure of CYP2C19 hetEMs were intermediate between that of PMs and homEMs. In the 30 mg group, CYP2C19 PMs exhibit significantly higher Cmax, AUCPK, and t1/2 than homEMs and presented remarkably higher AUCPK and t1/2 than those of CYP2C19 hetEMs. CYP2C19 hetEMs shows a significantly higher Cmax and AUCPK compared to CYP2C19 homEMs.
Article: The International SSRI Pharmacogenomics Consortium (ISPC): a genome-wide association study of antidepressant treatment response
Variant/haplotype: rs12729349
Drug(s): Selective serotonin reuptake inhibitors
Phenotype category: Efficacy
Significant: no
Association: Allele A is not associated with response to Selective serotonin reuptake inhibitors in people with Depressive Disorder, Major as compared to allele G.
Notes: The allele did not reach genome wide significance in the discovery or replication cohorts. GWA analyses were performed for two phenotypes: ‘% change in HRSD-17 score’ (% HRSD defined as the change in HRSD-17 score divided by the baseline score) and ‘response’ (defined as greater than or equal to 50% reduction in HRSD-17 score from baseline to 4-week visit).
Article: Role of Organic Cation Transporter 3 (SLC22A3) and Its Missense Variants in the Pharmacologic Action of Metformin
Gene: SLC22A3
Variant/haplotype: rs8187725
Drug(s): catecholamines, metformin
Phenotype category: Other, Metabolism/PK
Significant: yes
Association: Allele T is associated with decreased metabolism of catecholamines and metformin as compared to allele C.
Notes: In cells expressing the T variant, the uptake of these drugs was significantly reduced(about 80%).
Article: CYP3A4 genotype is associated with sildenafil concentrations in patients with heart failure with preserved ejection fraction
Gene: CYP3A4
Variant/haplotype: CYP3A4*1, CYP3A4*22
Drug(s): sildenafil
Phenotype category: Metabolism/PK
Significant: yes
Association: CYP3A4 *1/*22 is associated with increased concentrations of sildenafil in people with Heart Failure as compared to CYP3A4 *1/*1.
Notes: High-dose sildenafil in patients with heart failure with preserved left ventricular ejection fraction. Dose-adjusted peak concentrations were tested at week 12 and 24. p-value for significance was set at p<0.0167. Only significant in the subgroup of Caucasians, not in the whole patient population.