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Table 2 Non-HLA SSc susceptibility genes identified by the GWAS

From: Updates on genetics in systemic sclerosis

Gene SNP Study type References
Innate immunity
IRF4 rs9328192 GWAS [42]
IRF5 rs4728142, rs10488631, rs10488631, rs3757385, rs109542313, rs2004640, rs12537284, rs2280714 GWAS [42, 47,48,49,50, 46, 51]
IRF5-TNPO3 rs36073657, rs12155080 meta-GWAS [52]
IRF7 rs1131665, rs4963128, rs702966 CGA, meta-GWAS [52, 53]
IRF8 rs11642873, rs2280381, rs11117432, rs11644034, rs12711490, rs7202472, rs11117420 GWAS, meta-GWAS, [47, 50, 53,54,55,56, 52, 57]
TNFAIP3 rs5029929, rs2230926, rs6932056 GWAS [47, 50, 56, 58]
TNIP1 rs4958881, rs2233287, rs3792783 GWAS, meta-GWAS, [47, 49, 52, 59]
TAP2 rs12538892, rs17500468 ImmunoChip [51]
NFKB1 rs230534 meta-GWAS [52]
Adaptive immune response
TNFSF4 rs4916334, rs10798269, rs12039904 GWAS [47, 50, 60]
TNFSF4-LOC100506023-PRDX6 rs2022449, rs1857066 meta-GWAS [52]
CD247 rs2056626 GWAS, meta-GWAS [48, 52, 54, 61]
CSK rs1378942 GWAS, GWAS follow-up [47, 52, 60]
PTPN22 rs2476601 GWAS [42]
STAT4 rs7574865, rs3821236, rs4853458, rs10168266, rs3821236 GWAS, ImmunoChip, meta-GWAS [46, 49, 48, 50, 52, 54, 55]
BLK rs13277113, rs2736340 GWAS [47]
IL-12 Signaling Pathway and cytokines
IL-12A rs7758790, rs589446 GWAS, ImmunoChip [51, 52]
TYK2 rs2304256, rs34536443, rs12720356, rs35018800 ImmunoChip follow-up [62]
IL-12RB1 rs436857, rs2305743, rs8109496, rs11668601 meta-GWAS [52, 63]
IL-12RB2 rs3790566, rs924080, rs3790567 GWAS, meta-GWAS [52, 64]
Apoptosis, Autophagy Pathway
DNASEIL3 rs35677470 ImmunoChip [51]
FLNB-DNASE1L3-PXK rs7355798, rs4076852 meta-GWAS [52]
ATG5 rs9373839, rs633724 GWAS, ImmunoChip, meta-GWAS [42, 47, 51, 52]
PRDM1 rs4134466 GWAS [55]
GSDMA rs3894194 GWAS [65]
GSDMB rs883770 meta-GWAS [52]
NOTCH4 rs443198 GWAS [53]
Vascular homeostasis and fibrosis
PPARG rs310746 GWAS follow-up [66]
Other
NAB1 rs16832798 meta-GWAS [52]
DDX6 rs11217020 meta-GWAS [52]
DGKQ rs11724804 meta-GWAS [52]
POGLUT1-TIMMDC1-CD80-ARHGAP31 rs9884090 meta-GWAS [52]
RAB2A-CHD7 rs6598008 meta-GWAS [52]
TSPAN32, CD81-AS1 rs2651804 meta-GWAS [52]
NUP85-GRB2 rs1005714 meta-GWAS [52]