Table 4. Associations of candidate SNPs with SLE clinical phenotypes and autoantibodies in female SLE patients.
| SNP | Clinical Association (Sample 1 vs. Sample 2) | Sample Size Ratio | Genotypic Model | RAFa in Sample 1 | RAFa in Sample 2 | Pb | PFDRc | OR (95%CI) |
|---|---|---|---|---|---|---|---|---|
| TLR3 | ||||||||
| rs3775291 | Anti-dsDNA+ vs. Normal | 538:649 | GG vs. AA + AG | 715 (66.45%) | 822 (63.33%) | 0.0469 | 0.1408 | 1.26 (1.00–1.59) |
| Anti-SSB+ vs. Normal | 131:649 | Additive | 183 (69.85%) | 1132 (63.88%) | 0.0429 | 0.1288 | 1.35 (1.01–1.80) | |
| rs3775296 | Photosensitivity+ vs. Photosensitivity− | 167:560 | GG + GT vs. TT | 257 (76.95%) | 824 (73.57%) | 0.0244 | 0.1465 | 3.30 (1.17–9.30) |
| Pleural effusion+ vs. Pleural effusion− | 142:585 | Additive | 87 (30.63%) | 286 (24.44%) | 0.0317 | 0.1902 | 1.37 (1.03–1.83) | |
| Pleural effusion+ vs. Normal | 142:649 | Additive | 87 (30.63%) | 315 (24.27%) | 0.0238 | 0.0713 | 1.40 (1.05–1.86) | |
| Anemia+ vs. Anemia− | 236:491 | TT vs. GG + GT | 132 (27.97%) | 241 (24.54%) | 0.0041 | 0.0244 | 2.41 (1.33–4.39) | |
| Anemia+ vs. Normal | 236:649 | TT vs. GG + GT | 394 (83.47%) | 1067 (82.20%) | 0.0075 | 0.0373 | 2.11 (1.23–3.65) | |
| TLR7 | ||||||||
| rs3853839 | Oral ulcer+ vs. Normal | 194:649 | GG vs. CC + CG | 327 (84.28%) | 1016 (78.27%) | 0.0065 | 0.0196 | 1.62 (1.15–2.30) |
| Arthritis+ vs. Normal | 458:649 | GG vs. CC + CG | 767 (83.73%) | 1016 (78.27%) | 0.0012 | 0.0074 | 1.52 (1.18–1.96) | |
| Malar rash+ vs. Normal | 406:649 | GG vs. CC + CG | 674 (83.00%) | 1016 (78.27%) | 0.0061 | 0.0364 | 1.45 (1.11–1.88) | |
| Photosensitivity+ vs. Normal | 167:649 | Additive | 285 (85.33%) | 1016 (78.27%) | 0.0042 | 0.0251 | 1.63 (1.17–2.28) | |
| Pleural effusion+ vs. Normal | 142:649 | Additive | 237 (83.45%) | 1016 (78.27%) | 0.0498 | 0.0997 | 1.41 (1.00–1.99) | |
| Pericardial effusion+ vs. Pericardial effusion− | 83:644 | Additive | 147 (88.55%) | 1055 (81.91%) | 0.0363 | 0.2179 | 1.70 (1.04–2.79) | |
| Pericardial effusion+ vs. Normal | 83:649 | Additive | 147 (88.55%) | 1016 (78.27%) | 0.0022 | 0.0134 | 2.19 (1.33–3.61) | |
| Nephritis+ vs. Normal | 406:649 | GG vs. CC + CG | 667 (82.14%) | 1016 (78.27%) | 0.0196 | 0.1174 | 1.37 (1.05–1.77) | |
| Leukopenia+ vs. Normal | 410:649 | GG vs. CC + CG | 677 (82.56%) | 1016 (78.27%) | 0.0145 | 0.0723 | 1.38 (1.07–1.80) | |
| Anemia+ vs. Normal | 236:649 | Additive | 390 (82.63%) | 1016 (78.27%) | 0.0440 | 0.1141 | 1.33 (1.01–1.74) | |
| Complement depressed+ vs. Normal | 562:649 | GG vs. CC + CG | 937 (83.36%) | 1036 (78.48%) | 0.0013 | 0.0075 | 1.48 (1.17–1.88) | |
| Anti-dsDNA+ vs. Normal | 538:649 | GG vs. CC + CG | 895 (83.18%) | 1016 (78.27%) | 0.0019 | 0.0116 | 1.47 (1.15–1.87) | |
| Anti-Sm+ vs. Normal | 218:649 | GG vs. CC + CG | 366 (83.94%) | 1016 (78.27%) | 0.0032 | 0.0161 | 1.65 (1.19–2.31) | |
| Anti-RNP+ vs. Anti-RNP− | 255:472 | CC vs. CG + GG | 89 (17.45%) | 163 (17.27%) | 0.0330 | 0.1972 | 2.91 (1.10–7.73) | |
| Anti-RNP+ vs. Normal | 255:649 | GG vs. CC + CG | 421 (82.55%) | 1016 (78.27%) | 0.0090 | 0.0537 | 1.51 (1.11–2.06) | |
| Anti-SSA+ vs. Normal | 318:649 | GG vs. CC + CG | 528 (83.02%) | 1016 (78.27%) | 0.0050 | 0.0248 | 1.51 (1.13–2.01) | |
| Anti-SSB+ vs. Normal | 131:649 | GG vs. CC + CG | 217 (82.82%) | 1016 (78.27%) | 0.0299 | 0.0746 | 1.57 (1.05–2.36) | |
| rs5935436 | Neuropsychiatric manifestations+ vs. Neuropsychiatric manifestations− | 120:607 | Additive | 16 (6.67%) | 46 (3.79%) | 0.0498 | 0.2990 | 1.79 (1.00–3.19) |
| Neuropsychiatric manifestations+ vs. Normal | 120:649 | Additive | 16 (6.67%) | 46 (3.54%) | 0.0260 | 0.1559 | 1.96 (1.09–3.54) | |
| rs179010 | Discoid rash+ vs. Discoid rash− | 134:593 | TT vs. CC + CT | 106 (39.55%) | 433 (36.51%) | 0.0198 | 0.1189 | 1.77 (1.10–2.85) |
| Discoid rash+ vs. Normal | 134:649 | TT vs. CC + CT | 106 (39.55%) | 447 (34.44%) | 0.0113 | 0.0680 | 1.85 (1.15–2.98) | |
| Pleural effusion+ vs. Normal | 142:649 | Additive | 119 (41.90%) | 447 (34.44%) | 0.0198 | 0.0713 | 1.36 (1.05–1.76) | |
| Pericardial effusion+ vs. Normal | 83:649 | CT + TT vs. CC | 71 (42.77%) | 447 (34.44%) | 0.0344 | 0.1119 | 1.70 (1.04–2.76) | |
| Anti-SSA+ vs. Anti-SSA− | 318:409 | CT + TT vs. CC | 252 (39.62%) | 287 (35.09%) | 0.0006 | 0.0037 | 1.93 (1.33–2.81) | |
| Anti-SSA+ vs. Normal | 318:649 | Additive | 252 (39.62%) | 447 (34.44%) | 0.0280 | 0.0840 | 1.24 (1.02–1.51) | |
| TLR8 | ||||||||
| rs3764880 | Oral ulcer+ vs. Oral ulcer− | 194:533 | Additive | 343 (88.40%) | 885 (83.02%) | 0.0136 | 0.0816 | 1.55 (1.10–2.20) |
| Oral ulcer+ vs. Normal | 194:649 | Additive | 343 (88.40%) | 1067 (82.20%) | 0.0039 | 0.0232 | 1.66 (1.18–2.35) | |
| Arthritis+ vs. Arthritis− | 458:269 | GG vs. AA + AG | 787 (85.92%) | 441 (81.97%) | 0.0228 | 0.1369 | 1.47 (1.06–2.03) | |
| Arthritis+ vs. Normal | 458:649 | GG vs. AA + AG | 787 (85.92%) | 1067 (82.20%) | 0.0108 | 0.0325 | 1.41 (1.08–1.84) | |
| Pericardial effusion+ vs. Normal | 83:649 | GG vs. AA + AG | 145 (87.35%) | 1067 (82.20%) | 0.0446 | 0.1105 | 1.75 (1.02–3.02) | |
| Anti-SSB+ vs. Normal | 131:649 | Additive | 231 (88.17%) | 1067 (82.20%) | 0.0184 | 0.1105 | 1.63 (1.09–2.44) |
aRAF: Risk allele frequency.
bThe p-value was calculated from chi-square tests or Fisher's exact tests when appropriate.
cPFDR: The p-value was adjusted after the FDR correction.