Table 1. Association results and in silico analyses for the 18 previously confirmed (P<5×10-8) ulcerative colitis (UC) loci.
Left-right association boundaries are given for each index SNP (see Online Methods). RAF = risk allele frequency. OR is estimated using the meta-analysis cohort only. Known associations represent phenotypes previously associated with the locus at P<5×10-8). AS = ankylosing spondylitis, Ast = Asthma, BD = Behçet’s disease, CD = Crohn’s disease, CeD = celiac disease, Graves’ disease = GD, HL = Hodgkin’s lymphoma, MS = multiple sclerosis, PBC = primary biliary sclerosis, Ps = psoriasis, RA = rheumatoid arthritis, SLE = systemic lupus erythematosus, T1D = type 1 diabetes and WBC = white blood cell count. 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) | OR (95% CI) | Association reported with other phenotypes | Positional candidate genes of interest |
|---|---|---|---|---|---|---|---|---|
| rs6426833 | 1p36 | 19.93-20.18 | A | 0.541 | 3.93 × 10-35 | 1.30 (1.25-1.35) | ||
| rs11209026 | 1p31 | 67.30-67.54 | G | 0.935 | 5.12 × 10-28 | 1.74 (1.57-1.92) | CD, AS, BD, Ps | IL23R |
| rs1801274 | 1q23 | 159.54-159.91 | A | 0.505 | 2.16 × 10-20 | 1.21 (1.16-1.26) | SLE | FCGR2A, FCGR2B, HSPA6 |
| rs3024505 | 1q32 | 204.85-205.11 | A | 0.159 | 5.76 × 10-17 | 1.25 (1.19-1.32) | CD, BD, SLE, T1D | IL10, IL19 |
| rs7608910 | 2p16 | 60.76-61.87 | G | 0.390 | 1.70 × 10-14 | 1.19 (1.14-1.24) | CD, CeD, RA | PUS10 |
| rs4676406 | 2q37 | 241.20-241.32 | T | 0.516 | 8.32 × 10-11 | 1.14 (1.09-1.18) | GPR35 | |
| rs9822268 | 3p21 | 48.14-51.77 | A | 0.302 | 1.60 × 10-17 | 1.21 (1.16-1.26) | CD | MST1, UBA7, APEH, AMIGO3, GMPPB, BSN |
| rs17388568 | 4q27 | 123.20-123.78 | A | 0.273 | 9.49 × 10-7 | 1.12 (1.07-1.17) | CeD, T1D | IL21, IL2, ADAD1 |
| rs11739663 | 5p15 | 0.48-0.80 | T | 0.767 | 2.80 × 10-8 | 1.15 (1.09-1.21) | EXOC3 | |
| rs9268853 | 6p21 | 31.49-33.01 | T | 0.661 | 1.35 × 10-55 | 1.40 (1.34-1.47) | CD, CeD, GrD, MS, PBC, RA, T1D | HLA-DRB5, HLA-DQA1, HLA-DRB1, HLA-DRA, BTNL2 |
| rs4510766 | 7q22 | 107.20-107.39 | A | 0.559 | 2.00 × 10-16 | 1.20 (1.15-1.26) | ||
| rs6584283 | 10q24 | 101.25-101.33 | T | 0.472 | 8.46 × 10-21 | 1.21 (1.16-1.26) | CD | |
| rs7134599 | 12q14 | 66.72-66.92 | A | 0.385 | 1.06 × 10-16 | 1.19 (1.14-1.24) | IFNG, IL26 | |
| rs6499188 | 16q22 | 66.98-67.40 | A | 0.749 | 3.97 × 10-8 | 1.14 (1.09-1.20) | ZFP90 | |
| rs2872507 | 17q12 | 34.62-35.51 | A | 0.463 | 5.44 × 10-11 | 1.15 (1.10-1.19) | CD, Ast, PBC, T1D, WBC | IKZF3, ORMDL3, IKZF3, PNMT, ZPBP2, GSDML |
| rs6017342 | 20q13 | 42.49-42.70 | C | 0.538 | 1.09 × 10-20 | 1.20 (1.15-1.26) | HDL | SERINC3 |
| rs2836878 | 21q22 | 39.34-39.41 | G | 0.738 | 1.86 × 10-22 | 1.25 (1.20-1.32) | AS | |
| rs5771069 | 22q13 | 48.70-48.83 | G | 0.515 | 1.87 × 10-7 | 1.11 (1.07-1.16) | PIM3, IL17REL |