| Function | Gene | Replication | Largest Size (SSc/Control) | Reference |
|---|---|---|---|---|
| Immune Regulation | ||||
| HLA | yes | 1300/1000 for HLA alleles | [8-23, 11, 12]] | |
| STAT4 | yes | 2753/4569 | [11, 12, 25-27] | |
| CD247 | yes | 2753/4569 | [11, 33] | |
| TBX21 | replicated in a single study | 880/507 | [27] | |
| T cell | PTPN22 | inconsistent in subtype association | 1100/740 | [37-39] |
| differentiation | TNFSF4 | yes | 3014/3125 | [43, 44] |
| proliferation | IL23R | inconsistent reports | 1402/1038 | [48, 49] |
| activation | IL2RA | no | 3023/2735 | [151] |
| IL-21 | no | 4493/5856 | [52] | |
| SCHIP1IL12A | replicated in a single study | 4017/5935 | [137] | |
| CD226 | replicated in a single study | 991/1008 | [55] | |
| B cell signaling | BANK1 | yes | 2380/3270 | [57, 58] |
| C8orf13-BLK | yes | 1031/1014 | [59-61] | |
| innate immunity | PLD4 | no | 315/21054 | [63] |
| TLR-2 | replicated in a single study | 1170/925 | [65] | |
| NLRP1 | replicated in a single study | 1059/625 | [70] | |
| ATG5 | replicated in a single study | 4017/5935 | [137] | |
| Inflammation | ||||
| interferon regulation | IRF5 | yes | 2753/4569 | [11, 12, 73-75] |
| IRF8 | replicated in a single study | 3175/4971 | [123] | |
| NF-κB signaling | TNFAIP3 | yes | 1018/1012 | [77-79] |
| IRAK1 | inconsistent reports | 3065/2630 | [81, 82] | |
| NFKB1 | no | 5270 /8326 | [158] | |
| TNIP1 | replicated in a single study | 564/1776 | [12] | |
| cytokine/chemokine | FAS | inconsistent genotypes | 2900/3186 | [87, 88] |
| MIF | yes | 3800/4282 | [89, 90] | |
| HGF | no | 314/103 | [93] | |
| OPN | no | 357/864 | [98] | |
| IL-6 | no | 2749/3189 | [153] | |
| CXCL8 | no | 151/147 | [102] | |
| CCR6 | no | 2411/7084 | [105] | |
| CTGF | inconsistent reports | 500/500 | [107-111] | |
| regulation of monocytes | ITGAM | inconsistent reports | 4337/5326 | [114-116] |
| regulation of cytokines | CAV1 | replicated in a single study | 791/843 | [119] |
| Transcription | MECP2 | replicated in a single study | 3065/2630 | [82] |
| SOX5 | replicated in a single study | 3175/4971 | [123] | |
| JAZF1 | no | 6835/14274 | [165] | |
| DNA cleavage | DNASEIL3 | replicated in a single study | 4017/5935 | [137] |
| XRCC1 | no | 177 case only | [172] | |
| XRCC4 | no | 177 case only | [172] | |
| Kinase activity | PXK | no | 6835/14274 | [165] |
| CSK | no | 5270/8326 | [158] | |
| GRB10 | replicated in a single study | 3175/4971 | [123] | |
| Cell differentiation | NOTCH4 | replicated in a single study | 3175/4971 | [123] |
| Cell morphogenesis | RHOB | replicated in a single study | 564/1776 | [12] |
| Unknown | KIAA0319L | no | 6835/14274 | [165] |
| PSD3 | no | 5270/8326 | [158] | |
| PSOR1C1 | replicated in a single study | 564/1776 | [12] | |