TABLE IV.

Associations between power to detect association (based on training data) and replication status (P < 0.05 and association in the same direction as training data) in the testing dataset using twofold cross-validation

SNP set
LD features	Location	CV set	Number of SNPs analyzed	OR	95% CI	P
All SNPs	All	1	492,651	1.18	1.05–1.32	0.004
		2	492,651	1.19	1.07–1.33	0.002
	Exonica	1	136,424	1.15	0.93–1.41	0.20
		2	136,424	1.11	0.90–1.37	0.34
	Transcripta	1	274,680	1.20	1.04–1.40	0.01
		2	274,680	1.26	1.09–1.46	0.002
	Intergenic	1	217,971	1.15	0.97–1.36	0.12
		2	217,971	1.11	0.94–1.32	0.22
Pairwise r2 < 0.2	All	1	94,259	1.15	0.89–1.48	0.30
		2	94,259	1.08	0.84–1.40	0.54
	Exonica	1	26,295	1.43	0.91–2.26	0.13
		2	26,295	1.31	0.81–2.11	0.27
	Transcripta	1	52,719	1.32	0.94–1.84	0.11
		2	52,719	1.33	0.95–1.86	0.09
	Intergenic	1	41,540	0.95	0.64–1.42	0.81
		2	41,540	0.82	0.55–1.22	0.33

^aExon and transcript regions were extended on each side by 5 kb and 15 kb, respectively.

LD, linkage disequilibrium; CV, cross-validation; OR, odds ratio; CI, confidence interval.