Table 2. Association results and in silico analyses for the 29 newly confirmed ulcerative colitis (UC) loci.
UC loci that meet genome-wide significance P<5×10-8 in the combined analysis and P<0.05 in the replication study. Left-right association boundaries are given for each index SNP (see Online Methods). RAF = risk allele frequency. OR is estimated using the replication cohort only. Known associations represent phenotypes previously associated with the locus at P<5×10-8. AtD = atopic dermatitis, BMD = bone mineral density, CD = Crohn’s disease, CeD = celiac disease, Gli = glioma, Lep = leprosy, MS = multiple sclerosis, MyN = myeloproliferative neoplasms, PBC = primary biliary sclerosis, Ps = psoriasis, RA = rheumatoid arthritis and SLE = systemic lupus erythematosus. Candidate genes of interest are listed. Those in bold were highlighted by in silico analyses (GRAIL connectivity and/or presence of an eQTL or nonsynonymous SNP. See Online Methods and Supplementary Table 7 for more details).
| dbSNP ID | Chr. | Left-right(Mb) | Risk Allele | Allele frequency in controls | P-value (meta) | P-value (follow-up) | P-value (comb) | OR (95% CI) | Association reported with other phenotypes | Positional candidate genes of interest |
|---|---|---|---|---|---|---|---|---|---|---|
| rs734999 | 1p36 | 2.39-2.80 | C | 0.524 | 1.21 × 10-9 | 1.51 × 10-2 | 3.34 × 10-9 | 1.05 (1.01-1.09) | CeD, PBC | TNFRSF14, MMEL1, PLCH2, C1orf93 |
| rs35675666 | 1p36 | 7.83-8.13 | G | 0.829 | 1.09 × 10-8 | 1.13 × 10-2 | 4.84 × 10-9 | 1.08 (1.02-1.15) | CD | TNFRSF9, ERFFI1,UTS2,PARK7 |
| rs7524102 | 1p36 | 22.54-22.61 | A | 0.828 | 1.04 × 10-11 | 2.06 × 10-4 | 1.65 × 10-13 | 1.10 (1.05-1.16) | BMD | |
| rs7554511 | 1q32 | 199.06-199.33 | C | 0.721 | 2.04 × 10-13 | NA | NA | 1.19 (1.14-1.25) | CD, CeD | C1orf106 |
| rs2310173 | 2q11 | 101.66-102.13 | T | 0.461 | 8.44 × 10-8 | 5.94 × 10-6 | 3.17 × 10-12 | 1.09 (1.05-1.14) | IL1R2 | |
| rs11676348 | 2q35 | 218.58-218.97 | T | 0.486 | 8.78 × 10-9 | 6.18 × 10-4 | 1.25 × 10-10 | 1.07 (1.03-1.11) | IL8RA, SLC11A1, IL8RB, AAMP, ARPC | |
| rs267939 | 5p15 | 10.72-10.90 | C | 0.368 | 9.67 × 10-7 | 1.27 × 10-6 | 6.01 × 10-12 | 1.10 (1.06-1.15) | DAP | |
| rs3194051 | 5p13 | 35.83-36.07 | G | 0.269 | 2.19 × 10-6 | 2.06 × 10-3 | 4.22 × 10-8 | 1.07 (1.02-1.12) | MS | IL7R |
| rs6451493* | 5p13 | 40.32-40.85 | T | 0.610 | 1.78 × 10-6 | 2.09 × 10-4 | 2.80 × 10-9 | 1.08 (1.04-1.12) | CD, MS | PTGER4 |
| rs254560 | 5q31 | 134.41-134.53 | A | 0.397 | 3.06 × 10-7 | 4.19 × 10-4 | 1.25 × 10-9 | 1.07 (1.03-1.12) | ||
| rs6871626 | 5q33 | 158.46-158.86 | A | 0.334 | 1.02 × 10-8 | 1.40 × 10-14 | 1.11 × 10-21 | 1.17 (1.12-1.22) | CD, Ps, SLE | IL12B |
| rs943072 | 6p21 | 43.88-43.92 | G | 0.092 | 1.05 × 10-6 | 3.71 × 10-5 | 2.37 × 10-10 | 1.15 (1.08-1.23) | ||
| rs6911490 | 6q21 | 106.51-106.67 | T | 0.210 | 3.51 × 10-7 | 1.70 × 10-3 | 1.01 × 10-8 | 1.08 (1.03-1.13) | CD, RA, SLE | PDRM1 |
| rs6920220 | 6q23 | 137.88-138.17 | A | 0.207 | 6.38 × 10-10 | 1.94 × 10-8 | 8.05 × 10-17 | 1.14 (1.09-1.20) | CeD, Ps, RA, SLE | |
| rs798502 | 7p22 | 2.70-2.90 | A | 0.711 | 1.21 × 10-8 | 3.82 × 10-8 | 2.61 × 10-15 | 1.13 (1.08-1.18) | GNA12 | |
| rs4728142 | 7q32 | 128.33-128.56 | A | 0.444 | 1.68 × 10-6 | 1.25 × 10-3 | 1.74 × 10-8 | 1.07 (1.03-1.11) | SLE, RA, PBC | IRF5, TNPO3 |
| rs10758669 | 9p24 | 4.93-5.28 | C | 0.350 | 8.52 × 10-13 | 3.78 × 10-14 | 2.22 × 10-25 | 1.17 (1.12-1.21) | CD, MyN | JAK2 |
| rs4246905 | 9q32 | 116.48-116.74 | C | 0.713 | 4.77 × 10-8 | 1.44 × 10-5 | 5.65 × 10-12 | 1.10 (1.05-1.15) | CD, Lep | TNFSF8, TNFSF15 |
| rs10781499 | 9q34 | 138.27-138.55 | A | 0.411 | 6.95 × 10-13 | 2.50 × 10-8 | 2.62 × 10-19 | 1.12 (1.08-1.17) | CD | CARD9, INPP5E, SDCCAG3, SEC16A, SNAPC4 |
| rs12261843 | 10p11 | 35.22-35.94 | G | 0.286 | 2.35 × 10-8 | 1.22 × 10-3 | 7.09 × 10-10 | 1.07 (1.03-1.12) | CD | CCNY |
| rs907611 | 11q15 | 1.82-1.93 | A | 0.317 | 2.49 × 10-8 | 3.58 × 10-4 | 1.38 × 10-10 | 1.08 (1.03-1.13) | LSP1 | |
| rs2155219 | 11q13 | 75.72-76.02 | T | 0.500 | 6.33 × 10-8 | 1.61 × 10-9 | 5.39 × 10-16 | 1.13 (1.08-1.17) | CD, AtD | |
| rs678170 | 11q23 | 113.76-114.08 | A | 0.661 | 6.88 × 10-11 | 2.50 × 10-5 | 4.65 × 10-14 | 1.09 (1.05-1.14) | ||
| rs17085007 | 13q12 | 26.39-26.46 | C | 0.178 | 3.30 × 10-9 | 4.66 × 10-9 | 9.65 × 10-17 | 1.16 (1.10-1.21) | ||
| rs941823 | 13q13 | 39.90-39.95 | C | 0.756 | 3.93 × 10-7 | 1.93 × 10-6 | 3.82 × 10-12 | 1.12 (1.07-1.17) | ||
| rs16940202 | 16q24 | 84.53-84.58 | C | 0.180 | 1.27 × 10-12 | 1.42 × 10-8 | 5.96 × 10-19 | 1.15 (1.10-1.21) | MS | |
| rs2297441 | 20q13 | 61.66-61.98 | A | 0.766 | 5.78 × 10-8 | 2.68 × 10-4 | 1.70 × 10-10 | 1.09 (1.04-1.15) | CD, Gli | SLC2A4RG, STMN3, ZBTB46, ZGPAT, RTEL1, TNFRSF6B |
| rs1297265 | 21q21 | 15.62-15.77 | A | 0.564 | 1.73 × 10-7 | 5.02 × 10-7 | 6.99 × 10-13 | 1.11 (1.06-1.15) | CD | |
| rs2838519 | 21q22 | 44.41-44.52 | G | 0.390 | 2.26 × 10-8 | 7.10 × 10-4 | 6.41 × 10-11 | 1.14 (1.05-1.22) | CD | ICOSLG |