Table 2.

Association between UC and known CD loci.

				GWA STUDIES				REPLICATION			GWA + REPLICATION
Gene of interest	SNP from Barrett et al.	Chr#	CD meta p-value (Barrett et al.)	CEDARS	SWEDEN	NIDDK	Combined	ITALIAN	DUTCH	Combined	P-value	Notes
IL23R	rs11465804	1p31	6.38E-34	7.28E-04	1.47E-03	3.10E-05	5.91E-10	0.012	1.32E-03	5.18E-05	1.89E-13	1,2,4,5
ATG16L1	rs3828309	2q37	2.57E-21	0.24	0.18	0.25	0.57	0.28	0.63	0.67	0.48	1
MST1	rs3197999	3p21	2.17E-07	4.55E-03	2.00E-04	0.07	1.36E-06	1.90E-04	0.28	6.67E-04	3.76E-09	4
PTGER4	rs4613763	5p13	5.02E-22	0.57	0.62	0.0049	0.11	0.048	1.58E-03	2.81E-04	4.21E-04
IBD5	rs2188962	5q31	4.58E-09	0.14	0.40	0.32	0.35	0.044	2.50E-03	3.68E-04	2.90E-03	2
IRGM	rs13361189	5q33	8.17E-11	-	-	-	N/A	0.015	4.78E-05	4.33E-06	N/A
TNFSF15	rs4263839	9q32	2.61E-07	0.024	0.42	0.56	0.035	0.2996	2.85E-04	9.72E-04	2.01E-04	1,2
ZNF365	rs10995271	10q21	1.56E-07	0.024	0.73	0.89	0.24	0.1852	0.96	0.34	0.127	1
NKX2-3	rs11190140	10q24	1.71E-10	8.84E-04	0.028	0.058	1.85E-05	7.61E-06	0.37	1.45E-04	1.07E-08
NOD2 (R702W)	rs2066844	16q12	N/A	-	-	-	N/A	0.25	0.64	0.25	N/A
NOD2 (G908R)	rs2066845	16q12	N/A	-	-	-	N/A	0.69	0.017	0.049	N/A
NOD2 (insC)	rs2066847	16q12	N/A	-	-	-	N/A	0.90	0.077	0.18	N/A
NOD2 (R459R)	rs2066843	chr16	1.20E-27	0.36	0.99	0.62	0.41	-	-	N/A	N/A	3
PTPN2	rs2542151	18p11	6.54E-11	0.14	0.57	0.75	0.17	0.98	0.17	0.32	091	1
PTPN22	rs2476601	1p13	1.81E-05	0.11	0.32	0.096	0.19	0.25	0.15	0.067	0.88
ITLN1	rs2274910	1q23	3.51E-07	0.11	0.15	0.24	0.45	0.51	0.52	0.36	0.24	2
-	rs9286879	1q24	4.01E-07	0.90	0.75	0.85	0.71	0.19	0.063	0.70	0.60
KIF21B	rs11584383	1q32	1.94E-06	0.16	0.024	8.50E-02	1.88E-03	0.020	1.08E-04	1.17E-05	2.22E-07	1
IL12B	rs10045431	5q33	8.81E-09	-	-	-	N/A	0.024	0.023	1.39E-03	N/A
CDKAL1	rs6908425	6p22	2.53E-07	0.49	0.61	0.17	0.14	0.29	0.97	0.44	0.51
ATG5	rs7746082	6q21	3.13E-04	0.069	5.68E-03	0.042	1.34E-04	0.23	0.88	0.46	6.08E-04	1
CCR6	rs2301436	6q27	3.29E-07	0.044	0.16	0.094	3.30E-03	0.38	0.28	0.89	0.029
IKZF1	rs1456893	7p12	3.16E-05	0.93	0.66	0.53	0.960	0.15	1.14E-03	9.05E-04	0.040	1
-	rs1551398	8q24	4.90E-06	0.57	0.32	0.73	0.27	4.24E-04	0.057	0.25	0.90	2
JAK2	rs10758669	9p24	6.80E-07	0.023	0.028	0.49	2.88E-03	8.17E-04	0.023	7.06E-05	1.42E-06
CUL2/CREM	rs17582416	10p11	2.21E-05	0.69	0.028	0.92	0.15	0.032	0.45	0.040	0.016	1,2
C11orf30	rs7927894	11q13	1.43E-07	0.021	0.79	0.062	0.010	0.20	0.69	0.23	0.22	1
LRRK2, MUC19	rs11175593	12q12	1.33E-07	-	-	-	N/A	0.071	0.77	0.28	N/A
-	rs3764147	13q14	1.44E-05	0.27	0.010	0.041	0.34	0.59	0.76	0.55	0.27	1
ORMDL3	rs2872507	17q21	2.13E-06	3.93E-04	8.45E-04	0.18	2.06E-06	0.19	4.29E-03	3.22E-03	3.01E-08	1,4
STAT3	rs744166	17q21	5.94E-06	0.35	0.77	0.012	0.031	0.40	0.084	0.069	4.83E-03
-	rs1736135	21q21	3.28E-05	0.36	0.053	5.90E-04	2.88E-04	0.60	8.21E-07	1.15E-04	1.54E-07	1
ICOSLG	rs762421	chr21	1.08E-05	-	-	-	N/A	1.70E-03	0.59	9.32E-03	N/A	2
-	rs4807569	19p13	1.30E-08	0.99	0.53	0.058	0.15	-	-	N/A		1,3
GCKR	rs780094	2p23	7.24E-05	0.70	0.95	0.18	0.30	0.29	0.47	0.81	0.81	2
BTNL2, SLC26A3, HLA-DRB1, HLA-DQA1	rs3763313	6p21	1.45E-08	0.015	0.20	0.25	5.05E-03	0.020	0.71	0.17	0.19
PUS10	rs13003464	2p16	7.65E-06	0.012	2.41E-03	9.50E-05	4.67E-08	0.21	0.027	0.014	7.40E-09	4
CCL2, CCL7	rs991804	17q12	4.01E-06	0.52	0.060	0.46	0.25	0.013	0.028	9.33E-04	2.88E-03	2
LYRM4	rs12529198	6p25	7.08E-07	-	-	-	N/A	0.23	0.78	0.51	N/A
SLC22A23	rs17309827	6p25	2.08E-06	-	-	-	N/A	-	-	N/A	N/A	3
-	rs7758080	6q25	7.28E-06	0.67	0.18	0.54	0.38	0.50	0.079	0.44	0.84
-	rs8098673	18q11	3.17E-05	0.97	0.86	0.92	0.89	0.16	0.29	0.81	0.96
IL18RAP	rs917997	2q11	2.17E-05	0.58	0.58	0.012	0.15	0.35	0.026	0.025	0.011

Notes:

¹= Highly correlated proxies were evaluated in the UC GWA studies (See Supplementary Table 2 for further details)

²= Highly correlated proxies were typed in the Replication Stage (See Supplementary Table 2 for further details)

³= SNP assays failed to design or failed genotyping in Replication Stage

⁴= also reported in Table 1

⁵= rs11465804 was captured by the highly correlated proxy rs11209026 in both scan and replication (Table q and Supplementary Table 2)