Table 2.

Stepwise logistic regression starting with top 200 SNPs from joint case-control analysis, adjusted for admixture (first 2 principal components) and center

SNP	Chr	Position (Mb)	Minor allele	MAF (cases)	MAF (controls)	Single locus p valuea	Model	Stepwise p value	OR	95% CI
rs4331558	2p21	41.935	C	0.16	0.18	1.75E-05	Dom	6.01E-06	0.81	(0.73–0.88)
rs2303565	2q35	219.254	C	0.47	0.43	1.56E-06	Add	2.91E-07	1.17	(1.10–1.25)
rs1320900	3q22.1	133.196	A	0.31	0.34	6.92E-06	Dom	1.39E-06	0.81	(0.74–0.88
rs4917300	8q24.3	143.12	T	0.49	0.46	1.65E-06	Rec	1.16E-05	1.26	(1.14–1.40)
rs2453556	9p21.2	27.576	G	0.44	0.40	8.12E-07	Add	2.93E-07	1.18	(1.11–1.25)
rs1971791	15q23	68.363	G	0.49	0.47	9.70E-07	Rec	2.00E-06	1.28	(1.16–1.42)
rs8056742	16q24.1	83.650	C	0.13	0.11	4.91E-07	Add	8.68E-07	1.26	(1.15–1.39)
rs7477	17p11.2	16.187	T	0.52	0.48	2.89E-07	Rec	7.27E-07	1.29	(1.16–1.42)
rs9909055	17q11.2	23.620	T	0.22	0.25	1.60E-06	Dom	1.36E-06	0.81	(0.74–0.88)
rs2337186	18q11.2	19.566	G	0.37	0.33	2.24E-06	Add	1.16E-06	1.17	(1.10–1.25)
rs12608932	19p13.11	17.614	C	0.38	0.34	1.29E-07	Add	8.08E-08	1.19	(1.12–1.27)

Area under receiver operating characteristic curve for model without SNPs, C-statistic = 0.591. Difference in C-statistics for model adjusting for center and admixture versus model adjusting for center, admixture, and SNPs in table = 0.051. Model entry and exit criteria: 1 × 10⁻⁵. Area under receiver operating characteristic curve, C-statistic = 0.642, 10-fold cross-validation C-statistic = 0.635.

Key: Add, additive; Chr, chromosome; CI, confidence interval; Dom, dominant; kb, kilobases; MAF, minor allele frequency; Mb, megabase; OR, odds ratio; Rec, recessive; SNP, single nucleotide polymorphism.

^aSingle locus p value reflects statistical significance of the SNP in the joint analysis.