Table 3. Potentially novel loci from GWA scan.

Cytogenet. location	SNP	Location (hg18)	Gene/region	Disc. P	Disc. P (adj.)	Rep. P	Combined P	Minor allele	Freq cases	Freq. Controls	OR (95% C.I.)
1q21	rs6701216	151045150	EDC	0.0034	0.0053	0.0069	0.00005	T	0.174	0.127	1.45 (1.21,1.75)
2p11	rs2164807	85816062	GNLY-ATOH8	0.00084	0.0015	0.0039	0.000016	G	0.467	0.394	1.35 (1.18,1.54)
2p12	rs11126740	79754603	CTNNA2	0.0018	0.0018	0.019	0.00014	T	0.311	0.37	0.77 (0.67,0.88)
3q13	rs6804331	105237077	Gene desert	0.00073	0.0013	0.0455	0.0003	C	0.445	0.381	1.30 (1.13,1.50)
13q13	rs3812888	39128294	COG6	0.001	0.0017	4×10−4	0.00001	C	0.43	0.35	1.38 (1.15,1.66)
13q13	rs7993214	39248912	COG6	4.7×10−5	0.0001	0.0033	2×10−6	T	0.279	0.351	0.71 (0.62,0.82)
14q32	rs2282276	94730882	CLMN	0.0096	0.014	0.047	0.0031	G	0.099	0.073	1.40 (1.12,1.76)
15q21	rs4775912	49068271	USP8-TNFAIP8L3	0.00034	0.00065	0.0136	5.6×10−5	G	0.194	0.146	1.41 (1.19, 1.67)
15q21	rs3803369	49163121	USP8-TNFAIP8L3	0.00012	0.00025	0.0138	2.9×10−5	A	0.195	0.145	1.43 (1.21,1.69)

Trend P values from discovery, replication and combined analyses for U.S. PS samples (810 cases, 1256 controls) are shown. The minor allele, its frequency in cases and controls and its odds ratios and 95% C.I.s from the combined data-set are also shown. Abbreviations are described in footnotes to Table 1.