Table 2.
Non-HLA SSc susceptibility genes identified by the GWAS
| Gene | SNP | Study type | References |
|---|---|---|---|
| Innate immunity | |||
| IRF4 | rs9328192 | GWAS | [42] |
| IRF5 | rs4728142, rs10488631, rs10488631, rs3757385, rs109542313, rs2004640, rs12537284, rs2280714 | GWAS | [42, 47–50, 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, 53–56, 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] |