Table 3. Characteristics of 2 APOE SNPs and the top 5 SNPs selected by performance metrics in stage 2 (N = 619).

Gene	SNP	Nucleotide change	Chromosome/Location	HapMap or dbSNP MAF			Controls (n = 423)		Cases (n = 196)
				CEU	CHB	JPT	MAF	HWEP-value	MAF	HWE P-value
APOE	rs429358 (APOE112)	T → C	19/exon	0.15*	0.00	0.01	0.08	0.68	0.23	0.27
APOE	rs7412 (APOE158)	C → T	19/exon	0.08*	0.11	0.05	0.08	0.22	0.06	0.97
APOC1	rs4420638	G → A	19/3′UTR	0.18	0.12	0.07	0.11	0.93	0.23	0.75
CCDC81	rs10501617	T → C	11/intronic	0.40	0.20	0.16	0.27	0.37	0.26	0.64
ZNF521	rs7230380	A → C	18/intronic	0.47	0.49	0.50	0.50	0.90	0.48	0.36
ZNF521	rs12965520	T → C	18/intronic	0.50	0.45	0.50	0.50	0.58	0.48	0.33
CPXM2	rs2362967	C → T	10/intronic	0.26	0.50	0.58	0.48	0.03	0.48	0.78

Abbreviations: SNP, single nucleotide polymorphism; UTR, untranslated region; CEU, Utah residents with Northern and Western European ancestry from the CEPH collection; JPT, Japanese in Tokyo, Japan; CHB, Han Chinese in Beijing; MAF, minor allele frequency; HWE, Hardy-Weinberg equilibrium test.

*MAF data were obtained from dbSNP because the data were not available from the HapMap Project.