Table 2.

Newly confirmed associations (upper tier) and those with strong and replicated evidence for association (lower tier)

					WTCCC2 discovery sample			TASC discovery sample			Replication sample			Combined
Chr.	SNP ID	Positiona	Putative gene	Risk allele	P	OR	95% CI	P	OR	95% CI	P	OR	95% CI	P
1p36	rs11249215	25,169,771	RUNX3	A	2.1 × 10−5	1.19	1.10–1.28	0.00091	1.19	1.07–1.32	0.00029	1.15	1.07–1.24	9.2 × 10−11
5q33	rs6556416	158,751,323	IL12B	C	1.0 × 10−4	1.18	1.08–1.28	0.074	1.11	0.99–1.23	0.00018	1.17	1.08–1.27	1.9 × 10−8
12p13	rs11616188	6,373,003	LTBR- TNFRSF1A	A	1.2 × 10−5	1.21	1.11–1.31	6.2 × 10−8	1.38	1.23–1.56	0.0036	1.12	1.04–1.21	4.1 × 10−12
4q21	rs4389526	81,165,499	ANTXR2	A	0.00054	1.15	1.06–1.25	0.00027	1.21	1.09–1.34	0.019	1.1 0	1.02–1.19	9.4 × 10−8
5p13	rs10440635	40,526,547	PTGER4	A	0.0027	1.13	1.04–1.22	0.00020	1.20	1.09–1.32	0.017	1.1 0	1.02–1.19	2.6 × 10−7
9q34	rs10781500	138,389,159	CARD9	T	2.0 × 10−5	1.18	1.09–1.28	0.043	1.10	1.00–1.22	0.041	1.08	1.00–1.17	1.1 × 10−6
17q21	rs8070463	43,123,835	TBKBP1	C	0.0025	1.13	1.04–1.22	1.6 × 10−5	1.24	1.12–1.37	0.015	1.1 0	1.02–1.18	5.3 × 10−8

Top tier SNPs have a combined P < 5 × 10⁻⁸ and lower tier SNPs have combined P ≤ 5 × 10⁻⁶. Chr., chromosome.

^aNCBI human genome build 36 coordinates.