Table 1.
SNPs associated with GPA, listed in order of P-value.
| Chr | SNP | Disease(s)* | Gene(s) | A | WGGER | Toronto | S | Meta-analysis | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| OR (95% CI) | P | OR (95% CI) | P | OR (95% CI) | P† | ||||||
| 2 | rs3087243 | RA,T1D | CTLA4 | A | 0.80 (0.66–0.97) | 0.03 | 0.78 (0.67–0.91) | 0.001 | I | 0.79 (0.70–0.89) | 9.83E-05† |
| 2 | rs231735 | RA | CTLA4 | G | 0.84 (0.69–1.02) | 0.08 | 0.81 (0.70–0.94) | 0.005 | G | 0.82 (0.73–0.92) | 0.001 |
| 1 | rs2476601 | CD,Ps,RA,SLE,T1D | PTPN22 | A | 1.24 (0.92–1.69) | 0.16 | 1.41 (1.12–1.79) | 0.004 | G | 1.35 (1.12–1.62) | 0.002 |
| 20 | rs4810485 | RA | CD40 | T | 0.80 (0.64–1.01) | 0.05 | 0.81 (0.68–0.96) | 0.02 | I | 0.81 (0.70–0.92) | 0.002 |
| 1 | rs3766606 | Celiac | PARK7,DJ-1 | T | 0.79 (0.61–1.02) | 0.07 | 0.80 (0.66–0.98) | 0.03 | I | 0.80 (0.68–0.94) | 0.005 |
| 16 | rs4788084 | T1D | IL27 | T | 1.13 (0.94–1.37) | 0.19 | 1.21 (1.04–1.41) | 0.01 | G | 1.18 (1.05–1.33) | 0.006 |
| 16 | rs151181 | CD | IL27,others | C | 1.16 (0.96–1.40) | 0.12 | 1.20 (1.02–1.41) | 0.03 | I | 1.18 (1.05–1.34) | 0.007 |
| 10 | rs6584283 | CD,UC | NKX2-3 | T | 0.83 (0.69–1.00) | 0.05 | 0.87 (0.75–1.01) | 0.07 | I | 0.86 (0.76–0.96) | 0.009 |
| 1 | rs12727642 | Celiac | PARK7,TNFRSF9 | A | 0.81 (0.64–1.05) | 0.11 | 0.81 (0.66–1.00) | 0.05 | G | 0.81 (0.69–0.95) | 0.01 |
| 10 | rs11190140 | CD,UC | NKX2-3 | T | 0.85 (0.71–1.02) | 0.08 | 0.87 (0.75–1.01) | 0.07 | G | 0.86 (0.77–0.97) | 0.01 |
| 13 | rs9585056 | T1D | IDIN | C | 0.77 (0.62–0.96) | 0.02 | 0.91 (0.76–1.09) | 0.33 | I | 0.85 (0.74–0.98) | 0.03 |
| 15 | rs17574546 | T1D | RASGRP1 | C | 1.15 (0.92–1.44) | 0.21 | 1.20 (0.99–1.44) | 0.06 | I | 1.18 (1.02–1.36) | 0.03 |
| 11 | rs4963128 | SLE | PHRF1,KIAA1542 | T | 0.79 (0.64–0.97 | 0.02 | 0.92 (0.79–1.08) | 0.32 | G | 0.87 (0.77–0.99) | 0.03 |
| 6 | rs11755527 | T1D | BACH2 | G | 1.17 (0.97–1.42) | 0.10 | 1.12 (0.96–1.30) | 0.16 | I | 1.14 (1.01–1.28) | 0.03 |
| 9 | rs10758669 | CD | JAK2 | C | 1.16 (0.95–1.41) | 0.15 | 1.13 (0.97–1.32) | 0.12 | G | 1.14 (1.01–1.29) | 0.03 |
| 10 | rs706778 | RA | IL2RA | T | 1.11 (0.92–1.33) | 0.29 | 1.14 (0.98–1.33) | 0.09 | I | 1.13 (1.00–1.27) | 0.05 |
Abbreviations: Chr = chromosome; SNP = single nucleotide polymorphism designation; RA = rheumatoid arthritis; T1D = type 1 diabetes; CD = Crohn’s disease; Ps = psoriasis; SLE = systemic lupus erythematosus; UC = ulcerative colitis; A (in column heading) = allele used to calculate odds ratio; OR = odds ratio; CI = confidence interval; S = source of genotype in Toronto cohort (I = imputed, G = genotyped).
*
SNPs were included in genetic risk scores for the diseases listed.
†
Unadjusted P-values are shown. Only the top-ranked SNP had a P-value still <0.05 after adjustment for the false discovery rate (P*168/rank).