Spreadsheet: 131c1227-98c4-4af1-8836-59c9e5f9afd7
Sheet: nash.pathway.length

Table S6: List of SNP associated genes in pathways
pathway | Source | No. of genes in pathway | No. of SNPs in pathway | SNP-Genes in pathway
Biosynthesis of steroids | KEGG | 23 | 21 | CYP27B1,CYP51A1,DHCR24,DHCR7,FDFT1,FDPS,GGCX,GGPS1,HMGCR,HSD17B7,IDI1,IDI2,LSS,MVD,MVK,NQO1,PMVK,SC4MOL,SC5DL,SQLE,TM7SF2
Cholesterol biosynthesis | Reactome | 8 | 8 | FDFT1,GGPS1,HMGCS1,LSS,MVD,MVK,PMVK,SQLE
eukaryotic protein translation | BioCarta | 20 | 13 | EIF1,EIF2S1,EIF2S2,EIF3A,EIF4A1,EIF4A2,EIF4E,EIF4G1,EIF4G2,EIF4G3,EIF5,EIF5B,EIF6
Terpenoid biosynthesis | KEGG | 6 | 6 | FDFT1,FDPS,GGPS1,IDI1,IDI2,SQLE
Antigen processing and presentation | KEGG | 64 | 38 | CD74,CD8A,CD8B,CIITA,CREB1,CTSB,CTSL1,CTSS,HLA-DMA,HLA-DOB,HLA-DPA1,HLA-DQA2,HLA-DRB4,HLA-DRB5,HLA-F,HLA-G,IFNA1,IFNA10,IFNA13,IFNA16,IFNA17,IFNA2,IFNA5,IFNA6,IFNA8,KIR3DL2,KIR3DL3,KLRC1,KLRC4,KLRD1,LGMN,NFYA,[NAME],NFYC,RFX5,RFXAP,TAP1,TAP2
E2F transcription factor network | NCI-Nature | 72 | 57 | [NAME],CES1,CES2,CES3,CREBBP,DHFR,E2F1,E2F2,E2F3,E2F4,E2F5,E2F6,E2F7,EP300,KAT2B,MCL1,MCM3,MYBL2,MYC,PLAU,PRMT5,RANBP1,RB1,RBBP4,RBBP8,RBL1,RBL2,RRM2,RYBP,SERPINE1,SIRT1,SMARCA2,SP1,SULT2A1,TFDP1,TFDP2,TK1,TOPBP1,TP73,TRIM28,TRRAP,TYMS,WASF1,XRCC1,YY1
Ethanol is oxidized by NAD+ to form acetaldehyde, NADH, and H+ | Reactome | 6 | 6 | ADH1A,ADH1B,ADH1C,ADH4,ADH6,ADH7
Glycoprotein hormones | Reactome | 8 | 7 | CGA,CGB,CGB5,CGB8,FSHB,LHB,TSHB
Hormone ligand-binding receptors | Reactome | 11 | 10 | CGA,CGB,CGB5,CGB8,FSHB,FSHR,LHB,LHCGR,TSHB,TSHR
Pathogenic Escherichia coli infection | KEGG | 32 | 27 | ACTB,ACTG1,ARHGEF2,ARPC5,CD14,MC1R,RHOA,ROCK1,ROCK2,TLR4,TUBA1A,TUBA1B,TUBA1C,TUBA3D,TUBA3E,TUBA4A,TUBA8,TUBAL3,TUBB,TUBB1,TUBB2A,TUBB2B,TUBB3,TUBB4,TUBB4Q,TUBB6,WASL
Recycling of eIF2:GDP | Reactome | 8 | 5 | EIF2B1,EIF2B3,EIF2B5,EIF2S1,EIF2S2
1- and 2-Methylnaphthalene degradation | KEGG | 13 | 12 | ACAD9,ADH1A,ADH1B,ADH1C,ADH4,ADH5,ADH6,ADH7,LCLAT1,NAA20,NAT6,PNPLA3
3-Chloroacrylic acid degradation | KEGG | 13 | 13 | ADH1A,ADH1B,ADH1C,ADH4,ADH5,ADH6,ADH7,ALDH1B1,ALDH2,ALDH3A1,ALDH3A2,ALDH7A1,ALDH9A1
[NAME] mediated activation of jnk pathway via pyk2 dependent signaling | BioCarta | 34 | 28 | AGT,AGTR1,ATF2,BCAR1,CAMK2B,EGFR,FOS,GNAQ,GRB2,JUN,MAP2K1,MAP2K2,MAP3K1,MAPK1,MAPK3,MAPK8,MEF2A,MEF2C,MEF2D,PAK1,PLCG1,PRKCA,PRKCB,PTK2B,RAC1,RAF1,SOS1,SRC
B cell receptor signaling pathway | KEGG | 58 | 47 | AKT1,AKT2,AKT3,BLNK,CD22,CD79B,FCGR2B,FOS,GSK3B,IKBKB,INPP5D,JUN,KRAS,LILRB3,LYN,NFAT5,NFATC1,NFATC2,NFATC3,NFATC4,NFKB1,NFKBIA,NFKBIB,NFKBIE,NRAS,PIK3CA,PIK3CB,PIK3CD,PIK3CG,PIK3R1,PIK3R2,PIK3R3,PIK3R5,PPP3CA,PPP3CB,PPP3CC,PPP3R1,PRKCB,PTPN6,RAC1,RAC2,RASGRP3,RELA,SYK,[NAME]
BARD1 signaling events | NCI-Nature | 29 | 27 | ATM,ATR,BARD1,BRCA1,CCNE1,CDK2,CSTF1,EWSR1,FANCA,FANCC,[NAME],FANCF,FANCL,MRE11A,NBN,NPM1,PCNA,PRKDC,RAD50,RAD51,RBBP8,TOPBP1,TP53,UBE2D3,UBE2L3,XRCC6
Cell cycle | KEGG | 82 | 64 | ABL1,ATM,ATR,CCNB1,CCND1,CCND2,CCND3,CCNE1,CDC14A,CDC14B,CDC25A,CDC25B,CDC25C,CDC6,CDK1,CDK2,CDK4,CDK6,CDK7,CDKN1A,CDKN1C,CDKN2A,CDKN2B,CDKN2C,CHEK1,CHEK2,CREBBP,E2F1,E2F2,E2F3,EP300,ESPL1,GADD45B,[NAME],GSK3B,HDAC2,MCM2,MCM3,MCM5,MCM6,MCM7,MDM2,ORC2L,ORC3L,ORC4L,PCNA,PKMYT1,PRKDC,PTTG1,RB1,RBL1,RBL2,SMC1B,TFDP1,TGFB1,TGFB2,TP53,WEE1,YWHAB,YWHAE,YWHAG,YWHAH,YWHAQ,YWHAZ
cell cycle: g2/m checkpoint | BioCarta | 23 | 18 | ATM,ATR,BRCA1,CCNB1,CDK1,CDKN1A,CHEK1,CHEK2,EP300,MDM2,MYT1,PI4KA,PRKDC,RASGRF1,RPS6KA1,TP53,WEE1,YWHAH
Cellular roles of Anthrax toxin | NCI-Nature | 22 | 17 | ANTXR1,ANTXR2,CALM1,CALM2,CALM3,CARD17,CASP1,DEFA1,MAP2K1,MAP2K2,MAP2K3,MAP2K6,MAPK1,MAPK3,PGR,TNF,VCAM1
DNA strand elongation | Reactome | 9 | 6 | PCNA,POLA2,POLD2,POLD3,POLD4,PRIM1
Elongation of Intron-Containing Transcripts and co-transcriptional mRNA splicing | Reactome | 44 | 37 | [NAME],HNRNPD,HNRNPF,HNRNPH1,HNRNPK,HNRNPL,HNRNPM,HNRNPR,HNRNPU,METTL3,MNAT1,NCBP1,NCBP2,PCBP1,PCBP2,POLR2A,POLR2B,POLR2C,[NAME],POLR2E,POLR2F,POLR2G,POLR2H,POLR2J,PTBP1
ErbB signaling pathway | KEGG | 88 | 75 | ABL1,ABL2,AKT1,AKT2,AKT3,AREG,BAD,BRAF,BTC,CAMK2A,CAMK2B,[NAME],CAMK2G,CBLB,CBLC,CDKN1A,CRK,EGF,EGFR,EIF4EBP1,ERBB3,ERBB4,EREG,GAB1,GRB2,GSK3B,HBEGF,JUN,KRAS,MAP2K1,MAP2K2,MAPK1,MAPK10,MAPK3,MAPK8,MAPK9,MTOR,MYC,NCK1,NCK2,NRAS,NRG1,NRG2,NRG3,NRG4,PAK1,PAK2,PAK3,PAK4,PAK6,PAK7,PIK3CA,PIK3CB,PIK3CD,PIK3CG,PIK3R1,PIK3R2,PIK3R3,PIK3R5,PLCG1,PRKCA,PRKCB,PRKCG,PTK2,RAF1,RPS6KB1,SHC2,SHC3,SHC4,SOS1,SOS2,SRC,STAT5A,STAT5B,TGFA
Fatty acid biosynthesis | KEGG | 6 | 6 | ACACA,ACACB,FASN,MCAT,OLAH,OXSM
Folding of actin by CCT/TriC | Reactome | 10 | 9 | ACTB,CCT2,CCT3,CCT4,CCT5,CCT6A,CCT7,CCT8,TCP1
Galactose metabolism | KEGG | 26 | 22 | B4GALT1,B4GALT2,G6PC,G6PC2,GAA,[NAME],GALK1,GALK2,GALT,GCK,GLB1,HK1,HK2,HK3,LALBA,LCT,MGAM,PFKL,PFKM,PGM1,PGM2,UGP2
Gamma-carboxylation, transport, and amino-terminal cleavage of proteins | Reactome | 8 | 6 | F10,F2,F7,GAS6,PROC,PROS1
Gluconeogenesis | Reactome | 15 | 11 | FBP2,G6PC,GOT1,GOT2,GPI,MDH1,MDH2,PC,PCK1,PCK2,SLC25A10
growth hormone signaling pathway | BioCarta | 22 | 18 | GH1,GHR,[NAME],INSR,IRS1,JAK2,PIK3CA,PIK3R1,PLCG1,PRKCA,PRKCB,PTPN6,RPS6KA1,SLC2A14,SOS1,STAT5A,STAT5B
inhibition of matrix metalloproteinases | BioCarta | 8 | 7 | MMP14,MMP2,MMP9,RECK,TIMP2,TIMP3,TIMP4
intrinsic prothrombin activation pathway | BioCarta | 23 | 19 | COL4A1,COL4A2,COL4A3,COL4A4,F10,F11,F12,F2,F2R,F5,FGA,FGB,FGG,KLKB1,KNG1,PROC,PROS1,SERPING1,ZFHX3
lectin induced complement pathway | BioCarta | 12 | 12 | C2,C3,C5,C6,C7,C8A,C8B,C8G,C9,MASP1,MASP2,MBL2
links between pyk2 and map kinases | BioCarta | 26 | 22 | BCAR1,CAMK2B,GNAQ,GRB2,JUN,MAP2K1,MAP2K2,MAP2K3,MAP3K1,MAPK1,MAPK14,MAPK3,MAPK8,PAK1,PLCG1,PRKCA,PRKCB,PTK2B,RAC1,RAF1,SOS1,SRC
mitochondrial fatty acid beta-oxidation of unsaturated fatty acids | Reactome | 6 | 5 | ACADM,DCI,DECR1,HADHA,HADHB
mRNA Processing | Reactome | 9 | 7 | [NAME]
mRNA Splicing - Major [NAME] | Reactome | 106 | 79 | CCAR1,CD2BP2,CLP1,CPSF1,CPSF3,CPSF7,CSTF1,CSTF3,DDX23,DHX38,DHX9,DNAJC8,EFTUD2,GTF2F1,GTF2F2,HNRNPA0,HNRNPA1,HNRNPA2B1,HNRNPA3,HNRNPC,HNRNPD,HNRNPF,HNRNPH1,HNRNPK,HNRNPL,HNRNPM,HNRNPR,HNRNPU,HNRNPUL1,LSM2,MAGOH,NCBP1,NCBP2,NFX1,NHP2L1,PABPN1,PAPOLA,PCBP1,PCBP2,PHF5A,POLR2A,POLR2B,POLR2C,[NAME],POLR2E,POLR2F,POLR2G,POLR2H,POLR2J,PRPF4,PRPF6,PRPF8,PTBP1,RBM5,RBM8A,RNPS1,SF3A1,SF3A2,SF3A3,SF3B1,SF3B2,SF3B3,SF3B4,SF3B5,SFRS11,SNRNP200,SNRNP70,SNRPA,SNRPA1,SNRPB,SNRPB2,SNRPD2,SNRPD3,SNRPE,SNRPF,SRRM1,TXNL4A,U2AF1,U2AF2
[NAME]-regulation | Reactome | 7 | 6 | AP2B1,AP2M1,AP2S1,ARF1,ATP6V1H,LCK
Neuroactive ligand-receptor interaction | KEGG | 27 | 23 | CGA,CTSG,F2,F2R,F2RL1,F2RL2,F2RL3,FSHB,FSHR,GH1,GHR,GZMA,LEP,LEPR,LHB,LHCGR,PARD3,PLG,PRL,PRSS1,PRSS3,TSHB,TSHR
Nicotinate metabolism | Reactome | 12 | 11 | AFMID,HAAO,IDO1,KYNU,NADK,NADSYN1,NMNAT1,NMNAT2,NMNAT3,QPRT,TDO2
no2-dependent il-12 pathway in nk cells | BioCarta | 9 | 8 | IFNG,IL12A,IL12B,IL12RB1,JAK2,NOS2,STAT4,TYK2
nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells | BioCarta | 15 | 14 | GTF2A1,GTF2B,[NAME],HDAC3,KAT2B,NCOA1,NCOA2,NCOA3,NCOR2,NR3C1,POLR2A,RARA
O-Glycan biosynthesis | KEGG | 30 | 26 | B3GNT6,B4GALT5,C1GALT1,GALNT1,GALNT10,GALNT11,GALNT12,GALNT13,GALNT14,GALNT2,GALNT3,GALNT5,GALNT6,GALNT7,GALNT8,GALNT9,GALNTL1,GALNTL2,GALNTL4,GALNTL5,GALNTL6,GCNT1,GCNT3,GCNT4,ST3GAL1,ST6GALNAC1
p53 signaling pathway | BioCarta | 13 | 12 | BCL2,CCND1,CCNE1,CDK2,CDK4,CDKN1A,[NAME],RB1,TIMP3,TP53
pertussis toxin-insensitive ccr5 signaling in macrophage | BioCarta | 9 | 9 | CCL2,CCL4,CCR5,CXCL12,CXCR4,FOS,GNAQ,JUN,PLCG1
Processing of Capped Intron-Containing Pre-mRNA | Reactome | 35 | 30 | GTF2F1,GTF2F2,HNRNPA0,HNRNPA1,HNRNPA2B1,HNRNPA3,HNRNPC,HNRNPD,HNRNPF,HNRNPH1,HNRNPK,HNRNPL,HNRNPM,HNRNPR,HNRNPU,METTL3,NCBP1,NCBP2,PCBP1,PCBP2,POLR2A,POLR2B,POLR2C,[NAME],POLR2E,POLR2F,POLR2G,POLR2H,POLR2J,PTBP1
[NAME] signaling pathway | NCI-Nature | 29 | 25 | AKT1,ARHGEF2,CDK5,CDK5R1,DAB1,FYN,GRIN2A,GSK3B,ITGA3,ITGB1,LRP8,LRPAP1,MAP1B,MAP3K11,MAPK8,MAPK8IP1,MAPT,NCK2,PAFAH1B1,PIK3CA,PIK3R1,RAP1A,RAPGEF1,RELN,VLDLR
Regulation of CDC42 activity | NCI-Nature | 30 | 21 | APC,ARHGAP17,ARHGEF7,BCAR3,CDC42,DNMBP,DOCK10,DOCK6,DOCK9,FARP2,GIT1,ITSN1,ITSN2,MCF2L,NGEF,PLCG1,RACGAP1,RALBP1,SPATA13,VAV2,VAV3
Regulation of gene expression in beta cells | Reactome | 11 | 9 | FOXA2,FOXA3,FOXO1,HNF4G,MAFA,NKX2-2,NKX6-1,PDX1,SLC2A2
Regulation of Insulin Secretion by Glucagon-like Peptide-1 | Reactome | 10 | 9 | ADCY8,AKAP5,GCG,GLP1R,GNAS,IQGAP1,KCNJ11,SYT5,VAMP2
Regulation of the Fanconi anemia pathway | Reactome | 8 | 7 | FANCD2,FANCI,UBA52,UBB,UBC,USP1,ZBTB32
regulation of transcriptional activity by pml | BioCarta | 12 | 10 | CREBBP,DAXX,PAX3,PML,RB1,SIRT1,SP100,SUMO1,TP53,UBE2I
regulators of bone mineralization | BioCarta | 11 | 9 | ALPL,ANKH,COL4A1,COL4A2,COL4A3,COL4A4,ENPP1,IBSP,SPP1
rho cell motility signaling pathway | BioCarta | 32 | 28 | ARAP1,ARAP2,ARFGAP1,ARFGAP3,ARHGAP5,ARHGEF5,ASAP1,ASAP2,CACNA1A,CFL1,CHN1,DIAPH1,GSN,LIMK1,MYL2,MYLK,NCF2,PFN1,PIP5K1A,PIP5K1B,PPP1R12B,RALBP1,RHOA,ROCK1,TLN1,TRIO,VAV1,VCL
role of nicotinic acetylcholine receptors in the regulation of apoptosis | BioCarta | 17 | 14 | AKT1,BAD,CHRNB1,FASLG,FOXO3,MUSK,PIK3CA,[NAME],RAPSN,SRC,TERT,YWHAH
Signaling events mediated by Stem cell factor receptor (c-Kit) | NCI-Nature | 52 | 42 | AKT1,BAD,BCL2,CREBBP,EPO,FER,FOXO3,GAB1,GRAP2,GRB10,GRB2,GSK3B,JAK2,KIT,[NAME],LYN,MAP2K1,MAP2K2,MAP4K1,MAPK3,MAPK8,MATK,MITF,PIK3C2B,PIK3CA,PIK3R1,PTEN,PTPN11,PTPN6,PTPRO,RAF1,RPS6KB1,SH2B3,SNAI2,SOCS1,SOS1,SPRED1,SPRED2,STAT1,STAT3,STAT5A,[NAME]
Synthesis of bile acids and bile salts | Reactome | 10 | 7 | AKR1C4,AKR1D1,AMACR,CYP27A1,CYP7B1,CYP8B1,SLC27A2
Synthesis of bile acids and bile salts via 27-hydroxycholesterol | Reactome | 6 | 5 | [NAME]
Telomere C-strand (Lagging Strand) Synthesis | Reactome | 9 | 6 | PCNA,POLA2,POLD2,POLD3,POLD4,PRIM1
Trafficking of AMPA receptors | Reactome | 5 | 5 | AKAP5,DLG1,DLG4,EPB41L1,MDM2
trefoil factors initiate mucosal healing | BioCarta | 37 | 31 | AKT1,APAF1,BAD,CASP3,CASP6,CASP7,CASP9,CTNNB1,CYCS,EGFR,GH1,GHR,GRB2,IKBKB,MAP2K1,MAP2K2,MAPK1,MAPK3,MUC2,NFKB1,NFKBIA,PIK3CA,PIK3R1,RAF1,RELA,RHOA,RPS6KA1,SOS1,TFF1,TFF2,TFF3
Vibrio cholerae infection | KEGG | 47 | 39 | ACTA1,ACTA2,ACTB,ACTC1,ACTG1,ACTG2,ADCY3,ADCY9,ATP6V0A1,ATP6V0A2,ATP6V0A4,ATP6V0D1,ATP6V0D2,ATP6V0E1,ATP6V1A,ATP6V1B1,ATP6V1B2,ATP6V1C1,ATP6V1C2,ATP6V1E1,ATP6V1E2,ATP6V1F,ATP6V1G1,ATP6V1G2,ATP6V1G3,ATP6V1H,CFTR,ERO1L,GNAS,KCNQ1,PLCG1,PRKACA,PRKACB,PRKACG,PRKCA,PRKCB,PRKCG,SLC12A2,TCIRG1
Viral Messenger RNA Synthesis | Reactome | 65 | 46 | CCAR1,CD2BP2,DHX9,GTF2F1,GTF2F2,HNRNPA0,HNRNPA1,HNRNPA2B1,HNRNPA3,HNRNPC,HNRNPD,HNRNPF,HNRNPH1,HNRNPK,HNRNPL,HNRNPM,HNRNPR,HNRNPU,HNRNPUL1,NCBP1,NCBP2,NFX1,PCBP1,PCBP2,POLR2A,POLR2B,POLR2C,[NAME],POLR2E,POLR2F,POLR2G,POLR2H,POLR2J,PTBP1,RBM5,RNPS1,SNRNP70,SNRPA,SNRPB,SNRPD2,SNRPD3,SNRPE,SNRPF,SRRM1,U2AF1,U2AF2
Vitamins | Reactome | 6 | 5 | CYP24A1,CYP26A1,CYP26B1,CYP27B1,CYP2R1
Note:  For those pathways associated with 2 or more histologic features (Table 3), SNP associated gene in pathway are listed along with no. of genes and snps in pathway.