Table 2.
SLE risk SNPs association with clinical phenotypes
| SNP | Chr | Pos | Gene | RA | Phenotype | P D | P V | P C | OR (CI, 95%) |
|---|---|---|---|---|---|---|---|---|---|
| rs2476601 a | 1 | 114377568 | PTPN22 | A | Hematologic disorder | 0.0039 | 0.0433 | 5.20e-4 | 9.488 (1.310-68.726) |
| Antinuclear antibodies | 0.0146 | 0.0281 | 0.0011 | 0.168 (0.004-0.990) | |||||
| rs704840 | 1 | 173226195 | TNFSF4 | G | Renal disorder | 0.0407 | 0.9210 | 0.1290 | 1.199 (0.941-1.527) |
| rs3024505 | 1 | 206939904 | IL10 | T | Arthritis | 0.0325 | 0.1540 | 0.0170 | 1.557 (1.091-2.221) |
| rs3768792 | 2 | 213871709 | IKZF2 | C | Photosensitivity | 0.0437 | 0.3320 | 0.4580 | 0.893 (0.674-1.184) |
| Hematologic disorder | 0.0319 | 0.1880 | 0.0143 | 0.507 (0.301-0.855) | |||||
| rs9311676 | 3 | 58470351 | ABHD6,PXK | C | Oral ulcers | 0.0338 | 0.7960 | 0.9210 | 0.832 (0.674-1.028) |
| rs564799 | 3 | 159728987 | IL12A | C | Discoid rash | 0.0411 | 0.1410 | 0.6853 | 0.942 (0.674-1.316) |
| rs1270942 | 6 | 31918860 | MHC class III | C | Arthritis | 0.0138 | 0.6670 | 0.0407 | 1.530 (1.010-2.346) |
| rs9462027 | 6 | 34797241 | UHRF1BP1 | A | Malar rash | 0.0263 | 0.1730 | 0.0137 | 1.333 (1.071-1.660) |
| Oral ulcers | 0.0251 | 0.8950 | 0.0933 | 1.210 (0.971-1.508) | |||||
| rs6932056 | 6 | 138242437 | TNFAIP3 | C | Serositis | 0.0193 | 0.8140 | 0.1364 | 1.580 (0.898-2.781) |
| rs4917014 | 7 | 50305863 | IKZF1 | T | Oral ulcers | 0.0280 | 0.1550 | 0.5821 | 0.944 (0.753-1.184) |
| rs2663052 | 10 | 50069395 | WDFY4 | C | Neurologic disorder | 0.0370 | 0.1590 | 0.6311 | 0.963 (0.662-1.401) |
| rs4948496 | 10 | 63805617 | ARID5B | C | Malar rash | 0.0331 | 0.4580 | 0.3258 | 1.116 (0.906-1.375) |
| Photosensitivity | 0.0202 | 0.9480 | 0.0911 | 1.203 (0.977-1.483) | |||||
| rs2732549 | 11 | 35088399 | CD44 | T | Immunologic disorder | 0.0163 | 0.9910 | 0.0907 | 1.277 (0.976-1.670) |
| rs7941765 | 11 | 128499000 | ETS1,FLI1 | C | Arthritis | 0.0072 | 0.0701 | 0.0015 | 1.470 (1.151-1.877) |
| rs10774625 | 12 | 111910219 | SH2B3 | A | Serositis | 0.0207 | 0.0756 | 0.0038 | 0.715 (0.571-0.895) |
| Renal disorder | 0.0423 | 0.6410 | 0.0773 | 0.814 (0.650-1.018) | |||||
| Immunologic disorder | 0.0051 | 0.8190 | 0.0321 | 0.738 (0.566-0.964) | |||||
| rs1059312 | 12 | 129278864 | SLC15A4 | C | Serositis | 0.0253 | 0.2370 | 0.0156 | 1.321 (1.053-1.658) |
| rs4902562 | 14 | 68731458 | RAD51B | A | Renal disorder | 0.0130 | 0.8670 | 0.1010 | 0.834 (0.664-1.047) |
| rs2941509 | 17 | 37921194 | IKZF3 | A | Antinuclear Antibodies | 0.0304 | 0.0413 | 0.4943 | 0.676 (0.237-1.930) |
| rs2304256 | 19 | 10475652 | TYK2 | C | Arthritis | 0.0298 | 0.7690 | 0.1841 | 0.826 (0.622-1.096) |
A total of 19 SLE risk genetic variants were significantly associated with different systemic lupus erythematosus (SLE) phenotypes in the discovery stage. From these, the association between PTPN22 and hematologic disorder and between PTPN22 and the production of antinuclear antibodies (a) were significantly replicated in the validation cohort. Combining the statistical evidence from the two cohorts, seven additional genetic variants were found to be nominally associated with SLE phenotypes (shown in bold). Abbreviations: SNP single-nucleotide polymorphism, Chr chromosome, Pos SNP base pair in build GRCh37/hg19, RA disease risk allele, P D P value discovery cohort, P V P value validation cohort, P C P value combined, OR odds ratio according to the allele associated with disease risk, CI confidence interval (95%)