Table 3.

Results of genotyping 62 SNPs identified by sequencing in Set 1 samples (296 cases and 358 controls). InterSNP linkage disequilibrium is shown by r² for each SNP and the SNP immediately following. Association is shown for the 2 degree of freedom test (2DF) followed by the three genetic models, dominant (Dom), additive (Add), and recessive (Rec). MAF = minor allele frequency, HWE = Hardy Weinberg Equilibrium

	MAF				Genotypic Association
Marker	Cases	Controls	Prob HWE	r2	2 DF	Dom	Add	Rec
rs12052046	0.055	0.071	0.735	0	0.260	0.187	0.282	0.496
A-2318T	0.053	0.043	0.642	0.001	0.742	0.440	0.447	0.845
A-2243G	0.009	0.012	1.000	0.001	0.915	0.714	0.758	0.914
C-2222T	0.062	0.079	0.539	0.001	0.394	0.210	0.273	0.808
G-1969A	0.014	0.006	1.000	0.002	0.348	0.152	0.183	0.873
C-1962T	0.055	0.044	1.000	0	0.441	0.278	0.346	0.633
C-1921T	0.004	0.001	1.000	0	0.705	0.421	0.489	0.876
G-1846A	0.000	0.006	1.000	0.001	0.344	0.207	0.330	0.870
rs10404257	0.262	0.320	0.323	0.004	0.027	0.008	0.034	0.763
C-1547T	0.009	0.010	1.000	0	0.980	0.893	0.924	0.914
C-1291T	0.003	0.002	1.000	0	0.825	0.563	0.633	0.954
G-1201A	0.013	0.026	0.211	0	0.526	0.257	0.272	0.748
C-993T	0.004	0.004	1.000	0.002	0.982	0.909	0.949	0.920
C-850T	0.052	0.037	0.623	1	0.457	0.211	0.219	0.930
G-655A	0.052	0.037	0.623	0.003	0.463	0.216	0.224	0.931
G-197C	0.002	0.005	1.000	0	0.860	0.685	0.785	0.862
G-181A	0.002	0.002	1.000	0	0.948	0.744	0.758	0.871
A-163C	0.025	0.017	1.000	0	0.685	0.385	0.394	0.862
A-98C	0.022	0.005	1.000	0	0.049	0.001	0.025	0.842
T-85A	0.000	0.005	1.000	0	0.511	0.350	0.503	0.845
C52997T	0.025	0.017	1.000	0.016	0.609	0.321	0.335	0.911
rs2112649	0.484	0.425	0.936	0.054	0.113	0.101	0.010	0.077
G53218A	0.050	0.077	0.741	0.001	0.161	0.099	0.069	0.199
rs2287728	0.055	0.043	1.000	0	0.384	0.245	0.312	0.591
G57359A	0.000	0.003	1.000	0.082	0.613	0.423	0.571	0.918
rs2368475	0.025	0.017	1.000	0	0.615	0.325	0.340	0.912
A58329T	0.002	0.000	1.000	0	0.664	0.420	0.534	0.898
C58409T	0.007	0.010	1.000	0.001	0.902	0.700	0.753	0.899
rs11553600	0.066	0.085	0.158	0.027	0.511	0.254	0.248	0.617
rs3745859	0.222	0.266	1.000	0.038	0.163	0.057	0.074	0.547
G61654T	0.111	0.097	0.829	0.042	0.638	0.361	0.409	0.957
G62427A	0.005	0.004	1.000	0	0.968	0.799	0.807	0.929
C62517T	0.074	0.129	0.000	0	3.12E-4	0.166	0.008	1.03E-4
T62682G	0.002	0.000	1.000	0	0.685	0.443	0.558	0.915
G62719A	0.007	0.001	1.000	0	0.297	0.137	0.199	0.899
G62777A	0.005	0.004	1.000	0	0.954	0.758	0.768	0.914
T66655A	0.000	0.003	1.000	0	0.596	0.403	0.549	0.932
rs2306196	0.013	0.013	1.000	0	0.992	0.962	0.943	0.902
G69271A	0.000	0.001	1.000	0	0.842	0.674	0.796	0.926
C70315A	0.009	0.008	1.000	0	0.993	0.928	0.914	0.919
C70387T	0.004	0.003	1.000	0.001	0.965	0.789	0.799	0.913
rs7248577	0.051	0.064	1.000	2	0.519	0.449	0.361	0.322
C73985T	0.000	0.001	1.000	0	0.859	0.714	0.835	0.901
C74066T	0.060	0.085	0.069	0.002	0.194	0.078	0.112	0.947
rs2306197	0.019	0.023	0.239	0	0.820	0.794	0.696	0.534
C76085T	0.056	0.046	1.000	0.002	0.492	0.372	0.460	0.531
C76548T	0.011	0.006	1.000	0.002	0.618	0.334	0.373	0.914
rs12986337	0.055	0.042	0.389	0	0.512	0.248	0.253	0.915
G76867A	0.003	0.001	1.000	0	0.794	0.521	0.591	0.932
rs3786851	0.207	0.238	0.819	0.016	0.375	0.161	0.187	0.686
G77865A	0.057	0.048	0.684	0.967	0.284	0.322	0.475	0.311
rs12979947	0.055	0.045	1.000	0	0.510	0.356	0.432	0.593
G77942A	0.003	0.006	1.000	0	0.884	0.676	0.745	0.917
C78043T	0.005	0.004	1.000	0	0.970	0.805	0.813	0.931
rs1105759	0.065	0.058	0.717	0	0.645	0.509	0.588	0.579
G79206A	0.002	0.000	1.000	0	0.704	0.465	0.581	0.931
C79225T	0.007	0.009	1.000	2	0.965	0.838	0.878	0.913
C80196T	0.000	0.003	1.000	0	0.618	0.429	0.577	0.914
rs12981131	0.068	0.071	0.530	0.625	0.793	0.994	0.880	0.508
rs12974733	0.055	0.045	1.000	0.001	0.453	0.310	0.384	0.572
T82862A	0.016	0.007	1.000	2	0.337	0.146	0.175	0.915