Table 2. Loci with significant (p<5E-07) or suggestive (p between 5E-07 and 1E-05) evidence for association with anti–dsDNA + SLE identified in the joint analysis.
| Discovery dataset | Replication dataset | Joint analysis | ||||||||||
| 605 cases, 3334 controls | 206 cases, 1479 controls | 811 cases, 4813 controls | ||||||||||
| Gene/Region | chr | SNP | position | MA‡ | OR (95% CI) | p (λGC = 1.045) | OR (95% CI) | p(λGC = 1.038) | MAF‡ cases | MAF‡ controls | OR (95% CI) | p (λGC = 1.048) |
| TNXBa | 6 | rs1150754 | 32158736 | A | 2.05 (1.74–2.40) | 9.1E-18 | 2.77 (2.14–3.58)b | 1.4E-13b | 0.25 | 0.13 | 2.21 (1.93–2.53)c | 6.4E-29c |
| HLA-DR3a | 6 | rs2187668 | 32713862 | A | 2.14 (1.81–2.52) | 3.1E-18 | 2.54 (1.95–3.32) | 1.8E-11 | 0.22 | 0.12 | 2.23 (1.94–2.57) | 5.8E-28 |
| STAT4 | 2 | rs7574865 | 191790139 | T | 1.74 (1.51–1.99) | 2.3E-14 | 1.87 (1.49–2.36) | 1.7E-07 | 0.35 | 0.23 | 1.77 (1.57–1.99) | 2.0E-20 |
| IRF5 | 7 | rs10488631 | 128188134 | C | 1.73 (1.45–2.05) | 1.2E-09 | 2.52 (1.91–3.32) | 1.5E-10 | 0.19 | 0.11 | 1.92 (1.66–2.22) | 7.2E-18 |
| ITGAM | 16 | rs9888739 | 31220754 | T | 1.57 (1.33–1.86) | 2.8E-07 | 2.50 (1.93–3.24) | 1.1E-11 | 0.21 | 0.13 | 1.80 (1.56–2.07) | 1.1E-15 |
| BLK | 8 | rs2736340 | 11381382 | T | 1.30 (1.13–1.50) | 3.7E-04 | 1.59 (1.26–1.99) | 9.5E-05 | 0.30 | 0.23 | 1.38 (1.23–1.56) | 2.5E-07 |
| LAMC2 | 1 | rs525410 | 179908087 | G | 0.71 (0.62–0.8) | 2.5E-07 | 0.89 (0.72–1.1) | 0.30 | 0.45 | 0.51 | 0.75 (0.68–0.84) | 6.5E-07 |
| COL25A1 | 4 | rs4956211 | 110080730 | A | 1.41 (1.24–1.6) | 4.2E-07 | 1.14 (0.91–1.42)b | 0.27b | 0.42 | 0.35 | 1.33 (1.19–1.48)c | 1.1E-06c |
| PTTG1 | 5 | rs2431697 | 159812556 | C | 0.73 (0.64–0.84) | 6.8E-06 | 0.82 (0.66–1.01) | 0.069 | 0.37 | 0.44 | 0.76 (0.68–0.85) | 1.7E-06 |
| UBE2L3 | 22 | rs5754217 | 20264229 | T | 1.37 (1.17–1.60) | 9.7E-05 | 1.45 (1.14–1.84) | 0.0031 | 0.24 | 0.19 | 1.38 (1.21–1.57) | 1.9E-06 |
| SLC1A7 | 1 | rs6695567 | 53341606 | A | 0.80 (0.70–0.91) | 0.0010 | 0.70 (0.56–0.87) | 0.0015 | 0.37 | 0.43 | 0.76 (0.68–0.85) | 3.6E-06 |
| KIAA1542 | 11 | rs4963128 | 579564 | A | 0.78 (0.68–0.90) | 6.5E-04 | 0.66 (0.52–0.84) | 7.5E-04 | 0.27 | 0.34 | 0.75 (0.67–0.85) | 3.9E-06 |
| d | 1 | rs10737562 | 186455280 | A | 1.02 (0.90–1.16) | 0.77 | 0.36 (0.28–0.45)b | 4.1E-15b | 0.44 | 0.50 | 0.77 (0.69–0.86)c | 6.8E-06c |
Only the most significantly associated SNP per locus is displayed. Additional associated SNPs for each locus are presented in Table S2.
‡ MA = Minor allele, MAF = minor allele frequency.
a Only the most significantly associated MHC SNP and the HLA-DR3 tagSNP is included.
b imputed SNP, λGC = 1.089.
c imputed SNP, λGC = 1.071.
d No known gene within 100 kb.