Table 1.

IBD case-control association study results for GWA significant markers

Chr.	SNP	Position (B36)	Minor allele	MAF, affected	MAF, control	P value	Bonferonni P	OR	95% CI	Relevant gene
1	rs11209026	67478546	A	0.024	0.061	7.47 × 10−11	3.84 × 10−5	0.385	0.29–0.52	IL23R
16	rs5743289	49314275	T	0.232	0.172	3.77 × 10−10	0.00019	1.455	1.29–1.64	NOD2
1	rs11465804	67475114	G	0.030	0.065	1.46 × 10−9	0.00075	0.442	0.34–0.58	IL23R
6	rs477515	32677669	T	0.248	0.313	1.02 × 10−8	0.0052	0.724	0.65–0.81	HLA-DRB1
6	rs2516049	32678378	G	0.248	0.313	1.06 × 10−8	0.0054	0.724	0.65–0.81	HLA-DRB1
6	rs9271568	32698441	A	0.238	0.301	2.95 × 10−8	0.015	0.724	0.65–0.81	HLA-DQA1
9	rs6478109	116608587	A	0.251	0.314	3.20 × 10−8	0.016	0.733	0.66–0.82	TNFSF15
21	rs2836878	39387404	A	0.214	0.273	6.01 × 10−8	0.031	0.725	0.65–0.81	PSMG1
20	rs2315008	61814400	T	0.250	0.311	6.30 × 10−8	0.032	0.737	0.66–0.82	TNFRSF6B
20	rs4809330	61820030	A	0.249	0.310	6.95 × 10−8	0.036	0.738	0.66–0.82	TNFRSF6B
9	rs6478108	116598524	C	0.262	0.324	8.36 × 10−8	0.043	0.743	0.67–0.83	TNFSF15
16	rs2076756	49314382	G	0.317	0.258	9.65 × 10−8	0.050	1.332	1.20–1.48	NOD2

Newly identified signals are indicated in boldface. Minor allele frequencies (MAF), P values and odds ratios (OR) are shown. The ORs shown are for the minor alleles (as observed in the controls). Combined P values are also shown, together with the most relevant gene in which the markers reside or which they are nearest to. P values are two sided and uncorrected in each instance.