. Author manuscript; available in PMC: 2016 Sep 14.

Published in final edited form as: Nat Genet. 2016 Mar 14;48(5):510–518. doi: 10.1038/ng.3528

Table 1.

Bayesian logistic regression analysis identified 31 loci with 34 independent associations for which we determined a specific disease model constellation with high certainty (MeanProb_model≥0.6). A disease model is a list of diseases that a given locus is associated with (i.e. has a non-zero log odds ratio). Mean posterior probabilities (MeanProb) were calculated on a consensus-finding process of merging results from six different priors (Supplementary Table 3c, see Methods). Loci with very high certainty (MeanProb_model≥0.8) for the best disease model are shown in bold type. Out of the 34 associations with MeanProb_model≥0.6, 25 signals have 5 diseases involved, 6 signals have four diseases and 3 signals are unique to a single disease.

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.