Table 1.
GWA markers associated with SLE
| Gene | SNP | Chromosome | Position (Mb) | MAF (affected women) | MAF (controls) | Minor alleles | Set 1 P | Set 2 P | Set 3 P | Set 4 P | Overall joint P | OR | 95% CI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HLA region | rs3131379 | 6p21.33 | 31.829 | 0.197 | 0.103 | A | 8.02E-13 | 9.89E-14 | 1.06E-16 | 5.63E-12 | 1.71E-52 | 2.36 | 2.11–2.64 |
| HLA region | rsl270942 | 6p21.32 | 32.027 | 0.197 | 0.104 | G | 6.22E-12 | 1.11E-14 | 8.11E-17 | 1.72E-11 | 1.27E-51 | 2.35 | 2.10–2.63 |
| ITGAM | rs9888739 | 16pll.2 | 31.221 | 0.189 | 0.127 | T | 1.07E-04 | 2.16E-07 | 1.84E-06 | 3.00E-10 | 1.61E-23 | 1.62 | 1.47—1.78 |
| ITGAM | rsl143678 | 16pll.2 | 31.251 | 0.214 | 0.168 | T | 3.21E-03 | 4.78E-03 | 9.33E-06 | 2.12E-08 | 8.50E-14 | 1.40 | 1.28–1.53 |
| ITGAM | rs4548893 | 16pll.2 | 31.272 | 0.253 | 0.208 | A | 0.01 | 4.78E-03 | 1.84E-04 | 3.43E-08 | 2.36E-12 | 1.34 | 1.24—1.46 |
| IRF5/TNP03 | rs729302 | 7q32 | 128.356 | 0.261 | 0.315 | C | 4.28E-03 | 3.37E-03 | 1.07E-06 | 4.75E-04 | 2.00E-10 | 0.78 | 0.72–0.84 |
| IRF5/TNP03 | rsl0279821 | 7q32 | 128.471 | 0.267 | 0.325 | T | 0.05 | 9.69E-06 | 4.42E-06 | 5.16E-03 | 6.50E-09 | 0.80 | 0.74–0.86 |
| IRF5/TNP03 | rsl2537284 | 7q32 | 128.505 | 0.19 | 0.132 | A | 1.36E-05 | 2.06E-07 | 1.51E-04 | 1.08E-06 | 3.61E-19 | 1.54 | 1.40–1.70 |
| KIAA1542 | rs4963128 | llpl5.5 | 0.58 | 0.288 | 0.337 | T | 2.48E-03 | 3.72E-03 | 2.42E-03 | 1.38E-05 | 3.00E-10 | 0.78 | 0.73–0.85 |
| PXK | rs6445975 | 3pl4.3 | 58.345 | 0.323 | 0.276 | C | 1.80E-02 | 3.97E-02 | 1.19E-02 | 1.84E-05 | 7.10E-09 | 1.25 | 1.16–1.35 |
| - | rsl0798269 | lq25.1 | 171.576 | 0.304 | 0.356 | T | 0.04 | 1.66E-03 | 1.80E-03 | 0.023 | 1.11E-07 | 0.82 | 0.76–0.88 |
SNPs are listed that had P < 0.05 in each of the four sets and that exceeded P < 10−6 in the overall joint analysis. For the HLA, only the two most strongly associated SNPs are presented (Fig. 1 and Supplementary Fig. 3). The additive model is presented unless the test for lack of fit to an additive model was significant (P < 0.05), as for rs729302 in Set 1 (recessive). A secondary haplotype analysis did not improve the probabilities presented above for individual SNPs. MAF, minor allele frequency. Odds ratio (OR) is shown with 95% confidence interval (CI) boundaries. Positions are from build 35 throughout.