Table 1.
Locus | Signal | Chr | Locus_pos_L | Locus_pos_R | SNP | Nearby gene | OR(AS) | OR(CD) | OR(PS) | OR(PSC) | OR(UC) | Best model (VoteWinner) | VoteCount | MeanProb |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119 | 1 | 12 | 111702182 | 113030487 | rs3184504 | SH2B3 | 0.915 | 1.062 | 1.055 | 1.189 | 1.047 | PS_AS_CD_UC_PSC | 6 | 0.978 |
130 | 1 | 16 | 11018622 | 11496579 | rs367569 | TNP2 | 0.947 | 0.906 | 0.893 | 0.920 | 0.929 | PS_AS_CD_UC_PSC | 6 | 0.963 |
166 | 1 | 22 | 21811991 | 22076405 | rs2266961 | UBE2L3 | 1.104 | 1.136 | 1.089 | 1.070 | 1.082 | PS_AS_CD_UC_PSC | 6 | 0.961 |
155 | 1 | 20 | 31201111 | 31588992 | rs6058869 | DNMT3B | 1.091 | 1.060 | 1.071 | 1.062 | 1.060 | PS_AS_CD_UC_PSC | 6 | 0.953 |
91 | 1 | 10 | 6028491 | 6197536 | rs61839660 | IL2RA | 1.079 | 1.198 | 1.152 | 0.719 | 1.022 | PS_AS_CD_UC_PSC | 6 | 0.943 |
8 | 1 | 1 | 67301096 | 67942593 | rs80174646 | IL23R | 0.602 | 0.449 | 0.717 | 0.872 | 0.620 | PS_AS_CD_UC_PSC | 6 | 0.915 |
133 | 1 | 16 | 28289243 | 29025978 | rs26528 | IL27 | 1.126 | 1.152 | 1.049 | 1.076 | 1.082 | PS_AS_CD_UC_PSC | 6 | 0.91 |
39 | 1 | 2 | 241553993 | 241664801 | rs3749171 | GPR35 | 1.179 | 1.081 | 1.044 | 1.202 | 1.164 | PS_AS_CD_UC_PSC | 6 | 0.878 |
151 | 1 | 19 | 10364404 | 10625796 | rs74956615 | RAVER1 | 0.809 | 0.778 | 0.627 | 0.831 | 0.887 | PS_AS_CD_UC_PSC | 6 | 0.841 |
95 | 2 | 10 | 64284517 | 64759410 | rs10761648 | ZNF365 | 1.087 | 1.115 | 1.042 | 1.106 | 1.161 | PS_AS_CD_UC_PSC | 6 | 0.837 |
32 | 3 | 2 | 162960873 | 163358537 | rs35667974 | IFIH1 | 1.140 | 1.175 | 0.710 | 1.323 | 1.377 | PS_AS_CD_UC_PSC | 6 | 0.83 |
22 | 1 | 2 | 24684352 | 25594432 | rs13407913 | ADCY3 | 1.060 | 1.127 | 1.063 | 1.078 | 1.072 | PS_AS_CD_UC_PSC | 6 | 0.811 |
153 | 1 | 19 | 49092430 | 49278082 | rs679574 | FUT2 | 1.065 | 1.114 | 1.078 | 1.100 | 1.027 | PS_AS_CD_UC_PSC | 6 | 0.798 |
126 | 1 | 14 | 75698304 | 75749875 | rs1569328 | FOS | 0.936 | 0.902 | 0.913 | 0.912 | 0.950 | PS_AS_CD_UC_PSC | 6 | 0.791 |
151 | 4 | 19 | 10364404 | 10625796 | rs35074907 | KEAP1 | 1.115 | 1.294 | 1.133 | 1.318 | 1.147 | PS_AS_CD_UC_PSC | 6 | 0.788 |
103 | 2 | 11 | 57887309 | 58457495 | rs10750899 | OR5B21 | 1.232 | 1.208 | 1.067 | 1.319 | 1.357 | PS_AS_CD_UC_PSC | 6 | 0.767 |
143 | 1 | 17 | 57487538 | 58119648 | rs1292035 | RPS6KB1 | 1.101 | 1.109 | 1.100 | 1.044 | 1.071 | PS_AS_CD_UC_PSC | 5 | 0.711 |
147 | 1 | 18 | 12516768 | 12926278 | rs12968719 | PTPN2 | 1.116 | 1.241 | 1.056 | 1.120 | 1.144 | PS_AS_CD_UC_PSC | 5 | 0.699 |
32 | 4 | 2 | 162960873 | 163358537 | rs72871627 | IFIH1 | 1.277 | 1.153 | 0.646 | 1.139 | 1.473 | PS_AS_CD_UC_PSC | 5 | 0.693 |
62 | 4 | 5 | 158496825 | 158948962 | rs6556411 | AC008697.1 | 0.913 | 0.913 | 1.092 | 0.951 | 0.907 | PS_AS_CD_UC_PSC | 5 | 0.681 |
52 | 1 | 5 | 38800374 | 39031577 | rs395157 | OSMR | 0.961 | 0.911 | 0.949 | 0.917 | 0.921 | PS_AS_CD_UC_PSC | 5 | 0.678 |
48 | 1 | 4 | 103388565 | 104010837 | rs3774937 | NFKB1 | 1.120 | 0.992 | 1.041 | 1.167 | 1.107 | PS_AS_UC_PSC | 6 | 0.673 |
151 | 3 | 19 | 10364404 | 10625796 | rs12720356 | TYK2 | 1.085 | 1.083 | 0.775 | 0.897 | 1.101 | PS_AS_CD_UC_PSC | 4 | 0.673 |
8 | 4 | 1 | 67301096 | 67942593 | rs183686347 | IL23R | 1.773 | 2.725 | 1.357 | 1.142 | 1.887 | PS_AS_CD_UC_PSC | 5 | 0.664 |
71 | 1 | 6 | 159322326 | 159545322 | rs2451258 | - | 1.086 | 1.114 | 1.111 | 0.918 | 0.990 | PS_AS_CD_PSC | 4 | 0.658 |
151 | 2 | 19 | 10364404 | 10625796 | rs35018800 | TYK2 | 0.598 | 0.641 | 0.576 | 0.799 | 0.723 | PS_AS_CD_UC_PSC | 5 | 0.653 |
163 | 1 | 21 | 40413101 | 40483777 | rs9977672 | - | 0.825 | 0.920 | 1.006 | 0.786 | 0.799 | AS_CD_UC_PSC | 4 | 0.652 |
165 | 1 | 21 | 45596207 | 45702354 | rs4456788 | AP001057.1 | 1.081 | 1.135 | 0.993 | 1.126 | 1.110 | AS_CD_UC_PSC | 4 | 0.652 |
11 | 1 | 1 | 152534954 | 152860452 | rs6693105 | LCE3B | 0.994 | 0.998 | 0.799 | 1.006 | 1.006 | PS | 6 | 0.648 |
35 | 1 | 2 | 218877398 | 219266204 | rs11676348 | CXCR2 | 1.055 | 1.081 | 0.980 | 1.136 | 1.065 | AS_CD_UC_PSC | 4 | 0.638 |
160 | 1 | 20 | 62180117 | 62488635 | rs6062496 | TNFRSF6B | 1.000 | 0.872 | 0.962 | 0.923 | 0.877 | PS_CD_UC_PSC | 6 | 0.628 |
110 | 1 | 11 | 114256749 | 114589971 | rs661054 | NXPE1 | 0.984 | 0.998 | 0.982 | 0.993 | 0.883 | UC | 6 | 0.614 |
4 | 3 | 1 | 20060965 | 20304744 | rs4655215 | RNF186 | 0.976 | 0.989 | 0.974 | 0.994 | 1.171 | UC | 6 | 0.603 |
32 | 1 | 2 | 162960873 | 163358537 | rs2111485 | FAP | 1.030 | 1.054 | 0.852 | 1.074 | 1.082 | PS_AS_CD_UC_PSC | 5 | 0.6 |
Locus: number of locus defined by annotation of association boundaries (see Methods); Signal: number of independent signal (from conditional analysis) within a certain locus; Chr: chromosome; Locus_pos_l/Locus_pos_r: left/right association boundaries for locus (see Methods section). Genomic positions were retrieved from NCBI's dbSNP build v142 (genome build hg19); SNP: rs ID; Nearby gene: gene candidate nearest to the index SNP as long as a gene was with 10kb of the SNP; OR: single disease odds ratio: Ankylosing spondylitis (AS), Crohn's disease (CD), psoriasis (PS), primary sclerosing cholangitis (PSC) and ulcerative colitis (UC). Best model (VoteWinner): disease model with highest posterior probability under six different priors (Supplementary Table 3c); VoteCount: we counted how many priors voted for that model, and calculated the mean posterior from six different priors; MeanProb: Mean posterior probability (MeanProbmodel) for the proposed model and risk variant of six different priors.