Association results for SLE risk variants genotyped in UK RA cases and controls
| Chr | Locus | SNP | Major allele/minor allele | MAF cases | MAF controls | HWE controls | Trend test p value | Corrected p value | Allelic OR (95% CI) |
|---|---|---|---|---|---|---|---|---|---|
| 1 | TNFSF4 | rs10489265 | T/G | 0.25 | 0.24 | 0.56 | 0.11 | 1.05 (0.99 to 1.12) | |
| 4 | BANK1 | rs10516487 | C/T | 0.31 | 0.31 | 0.66 | 0.52 | 0.98 (0.93 to 1.04) | |
| 5 | TNIP1 | rs10036748 | C/T | 0.24 | 0.24 | 0.21 | 0.46 | 1.02 (0.96 to 1.09) | |
| 5 | PTTG1 | rs2431697 | T/C | 0.42 | 0.43 | 0.62 | 0.06 | 0.95 (0.90 to 1.00) | |
| 6 | UHRF1BP1 | rs11755393 | A/G | 0.34 | 0.34 | 0.41 | 0.79 | 1.01 (0.95 to 1.07) | |
| 6 | ATG5 | rs6568431 | C/A | 0.41 | 0.39 | 0.27 | 0.02 | 0.22 | 1.07 (1.01 to 1.13) |
| 7 | JAZF1 | rs864745 | G/A | 0.49 | 0.49 | 0.98 | 0.20 | 1.03 (0.98 to 1.08) | |
| 8 | BLK | rs2736340 | C/T | 0.26 | 0.24 | 0.95 | 3.0×10−4 | 3.3×10−3 | 1.11 (1.05 to 1.17) |
| 11 | KIAA1542 | rs4963128 | G/A | 0.32 | 0.34 | 0.96 | 0.02 | 0.22 | 0.93 (0.88 to 0.99) |
| 16 | ITGAM | rs9888739 | C/T | 0.10 | 0.11 | 0.42 | 0.16 | 0.94 (0.85 to 1.03) | |
| 22 | UBE2L3 | rs5754217 | G/T | 0.21 | 0.19 | 0.37 | 2.4×10−3 | 0.026 | 1.11 (1.04 to 1.19) |
Linkage disequilibrium between the genotyped and reported variant (in brackets), when different: TNFSF4(rs2205960): r2=0.95; TNIP1(rs7708392): r2=0.90; PTTG1(rs2431099): r2=0.60; JAZF1(rs849142): r2=1; ITGAM(rs11860650): r2=0.92.
Chr, chromosome; CI, confidence interval; HWE, Hardy–Weinberg equilibrium; MAF, minor allele frequency; OR, odds ratio; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; SNP, single nucleotide polymorphism.