Table 1.

Crohn’s disease-specific, ulcerative colitis-specific and IBD general loci

Chr	Position (hg19 (Mb))	SNP	Key Genes (+N additional in locus)
Crohn’s Disease
1	78.62	rs17391694	(5)
1	114.3	rs6679677§	PTPN22||,(8)
1	120.45	rs3897478	ADAM30,(5)
1	172.85	rs9286879	FASLG,TNFSF18,(0)
2	27.63	rs1728918	UCN,(23)
2	62.55	rs10865331	(3)
2	231.09	rs6716753	SP140,(5)
2	234.15	rs12994997	ATG16L1||, (8)
4	48.36	rs6837335	(6)
4	102.86	rs13126505	(1)
5	55.43	rs10065637	IL6ST,IL31RA,(1)
5	72.54	rs7702331	(4)
5	173.34	rs17695092	CPEB4,(2)
6	21.42	rs12663356	(3)
6	31.27	rs9264942	(22)
6	127.45	rs9491697	(3)
6	128.24	rs13204742	(2)
6	159.49	rs212388	TAGAP,(5)
7	26.88‡	rs10486483	(2)
7	28.17	rs864745	CREB5,JAZF1,(1)
8	90.87	rs7015630	RIPK2,(4)
8	129.56	rs6651252	0
13	44.45	rs3764147	LACC1,(3)
15	38.89	rs16967103	RASGRP1,SPRED1,(2)
16	50.66**	rs2066847§	NOD2||, (6)
17	25.84	rs2945412	LGALS9,NOS2,(3)
19	1.12	rs2024092	GPX4,HMHA1,(20)
19	46.85‡	rs4802307	(9)
19	49.2	rs516246	FUT2, (25)
21	34.77	rs2284553	IFNGR2,IFNAR1, (10)
Ulcerative Colitis
1	2.5	rs10797432	TNFRSF14, (10)
1	20.15**	rs6426833	(9)
1	200.09	rs2816958	(3)
2	198.65	rs1016883	RFTN2,PLCL1,(7)
2	199.70*	rs17229285	0
3	53.05	rs9847710	PRKCD,ITIH4,(8)
4	103.51	rs3774959	NFKB1,MANBA,(2)
5	0.59	rs11739663	SLC9A3,(8)
5	134.44	rs254560	(6)
6	32.595	rs6927022	(15)
7	2.78	rs798502	CARD11, GNA12, (5)
7	27.22‡	rs4722672	(14)
7	107.45*	rs4380874	DLD,(9)
7	128.57	rs4728142	IRF5||, (13)
11	96.02	rs483905	JRKL,MAML2,(2)
11	114.38	rs561722	FAM55A,FAM55D,(5)
15	41.55	rs28374715	(11)
16	30.47	rs11150589	ITGAL,(20)
16	68.58	rs1728785	ZFP90,(6)
17	70.64	rs7210086	(3)
19	47.12‡	rs1126510	CALM3,(14)
20	33.8	rs6088765	(11)
20	43.06	rs6017342	ADA,HNF4A,(9)
Inflammatory Bowel Disease
1	1.24	rs12103	TNFRSF18,TNFRSF4,(30)
1	8.02	rs35675666	TNFRSF9,(6)
1	22.7	rs12568930†	(3)
1	67.68**	rs11209026†	IL23R||, (5)
1	70.99	rs2651244†	(3)
1	151.79	rs4845604†	RORC,(14)
1	155.67	rs670523†	(31)
1	160.85	rs4656958†	CD48, (15)
1	161.47	rs1801274†	FCGR2A/B, FCGR3A, (13)
1	197.6	rs2488389	C1orf53,(2)
1	200.87	rs7554511	KIF21B,(6)
1	206.93	rs3024505†	IL10, (10)
2	25.12	rs6545800†	ADCY3,(6)
2	28.61	rs925255†	FOSL2,BRE,(1)
2	43.81	rs10495903†	(5)
2	61.2	rs7608910	REL, (9)
2	65.67	rs6740462	SPRED2,(1)
2	102.86*	rs917997†	IL18RAP, IL1R1, (7)
2	163.1	rs2111485	IFIH1,(5)
2	191.92	rs1517352	STAT1,STAT4,(2)
2	219.14	rs2382817	(15)
2	241.57*	rs3749171†	GPR35,(12)
3	18.76	rs4256159†	0
3	48.96**	rs3197999	MST1, PFKB4, (63)
4	74.85	rs2472649†	(11)
4	123.22	rs7657746	IL2,IL21,(2)
5	10.69	rs2930047	DAP,(2)
5	40.38**	rs11742570†	PTGER4,(1)
5	96.24	rs1363907	ERAP2, ERAP1, (3)
5	130.01	rs4836519†	(1)
5	131.19*	rs2188962†	IBD5 locus, (18)
5	141.51	rs6863411†	SPRY4,NDFIP1,(5)
5	150.27	rs11741861†	IRGM||, (10)
5	158.8**	rs6871626†	IL12B,(3)
5	176.79	rs12654812	DOK3,(17)
6	14.71	rs17119	0
6	20.77*	rs9358372†	(2)
6	90.96	rs1847472	(1)
6	106.43	rs6568421†	(2)
6	111.82	rs3851228	TRAF3IP2, (4)
6	138	rs6920220†	TNFAIP3,(1)
6	143.9	rs12199775	PHACTR2,(5)
6	167.37	rs1819333†	CCR6,RPS6KA2,(4)
7	50.245*	rs1456896	ZPBP,IKZF1,(4)
7	98.75	rs9297145	SMURF1,(6)
7	100.34	rs1734907†	EPO,(21)
7	116.89	rs38904†	(6)
8	126.53	rs921720†	TRIB1,(1)
8	130.62	rs1991866	(2)
9	4.98	rs10758669	JAK2,(4)
9	93.92	rs4743820†	NFIL3,(2)
9	117.60**	rs4246905	TNFSF15, (4)
9	139.32*	rs10781499†	CARD9, (22)
10	6.08	rs12722515†	IL2RA,IL15RA,(6)
10	30.72	rs1042058†	MAP3K8,(3)
Inflammatory Bowel Disease
10	35.3	rs11010067†	CREM,(3)
10	59.99	rs2790216	CISD1,IPMK,(2)
10	64.51**	rs10761659†	(3)
10	75.67	rs2227564†	(13)
10	81.03	rs1250546†	(5)
10	82.25	rs6586030†	TSPAN14,C10orf58,(4)
10	94.43	rs7911264	(4)
10	101.28	rs4409764	NKX2-3,(6)
11	1.87	rs907611	TNNI2,LSP1,(17)
11	58.33	rs10896794	CNTF,LPXN,(8)
11	60.77	rs11230563	CD6, (14)
11	61.56	rs4246215†	(15)
11	64.12	rs559928	CCDC88B,(23)
11	65.65	rs2231884†	RELA, (25)
11	76.29	rs2155219†	(5)
11	87.12	rs6592362	(1)
11	118.74	rs630923†	CXCR5,(17)
12	12.65	rs11612508†	LOH12CR1,(8)
12	40.77*	rs11564258†	MUC19,(1)
12	48.2	rs11168249†	VDR,(8)
12	68.49	rs7134599†	IFNG, (3)
13	27.52	rs17085007†	(2)
13	40.86**	rs941823†	(3)
13	99.95	rs9557195	GPR183,GPR18,(6)
14	69.27	rs194749†	ZFP36L1,(4)
14	75.7	rs4899554†	FOS,MLH3,(6)
14	88.47	rs8005161	GPR65,GALC,(1)
15	67.43	rs17293632†	SMAD3,(2)
15	91.17	rs7495132	CRTC3,(3)
16	11.54*	rs529866†	SOCS1,LITAF, (11)
16	23.86	rs7404095	PRKCB,(5)
16	28.6	rs26528†	IL27, (14)
16	86	rs10521318†	IRF8,(4)
17	32.59	rs3091316†	CCL13,CCL2, (5)
17	37.91	rs12946510	ORMDL3, (16)
17	40.53	rs12942547†	STAT3, (15)
17	57.96	rs1292053†	TUBD1,RPS6KB1,(9)
18	12.8	rs1893217†	(6)
18	46.39	rs7240004†	SMAD7,(2)
18	67.53	rs727088	CD226,(2)
19	10.49*	rs11879191	TYK2, (27)
19	33.73	rs17694108	CEBPG,(8)
19	55.38	rs11672983	(19)
20	30.75	rs6142618†	HCK,(10)
20	31.37	rs4911259	DNMT3B,(8)
20	44.74	rs1569723†	CD40, (13)
20	48.95	rs913678	CEBPB,(5)
20	57.82	rs259964	ZNF831,CTSZ,(5)
20	62.34	rs6062504	TNFRSF6B, (26)
21	16.81	rs2823286†	0
21	40.46	rs2836878†	(3)
21	45.62	rs7282490	ICOSLG,(9)
22	21.92	rs2266959	(13)
22	30.43	rs2412970	LIF, OSM, (9)
22	39.69*	rs2413583†	(19)

The position given is the middle of the locus window.

^*= additional genome-wide significant associated SNP in the region.

^**= two or more additional genome-wide significant SNPs in the region.

^‡ = These regions have overlapping but distinct UC and CD signals.

^† = heterogeneity of odds ratios.

^§ = CD risk allele is significantly protective in UC.

^||= gene for which functional studies of associated alleles have been reported. Newly discovered loci. Bolded rs numbers indicate SNPs with p-values less than 10⁻¹³. Listed are genes implicated by one or more candidate genes approaches. Bolded genes have been implicated by two or more candidate gene approaches. For each locus, the top two candidate genes are listed. A complete listing of gene prioritization is provided in Supplementary Table 2.