TABLE V.

Proportion of SNPs replicating (P < 0.05 and with the same direction) in the testing dataset according to power estimated from the training dataset using twofold CV

SNP set		CVset	Number of SNPs analyzed	Quintiles of power					Top decile of power (>0.38)
LD features	Location			Q1 (≥0.05)	Q2 (0.06–0.08)	Q3 (0.09–0.13)	Q4 (0.14–0.25)	Q5 (>0.25)
All SNPs	All	1	492,651	2.51	2.65	2.55	2.63	2.71	2.80
		2	492,651	2.43	2.62	2.51	2.62	2.68	2.72
	Exonica	1	136,424	2.69	2.70	2.51	2.95	2.80	2.85
		2	136,424	2.56	2.53	2.55	2.51	2.70	2.70
	Transcripta	1	274,680	2.67	2.69s	2.56	2.67	2.83	2.90
		2	274,680	2.46	2.56	2.47	2.56	2.72	2.78
	Intergenic	1	217,971	2.31	2.61	2.53	2.59	2.55	2.67
		2	217,971	2.40	2.69	2.57	2.67	2.66	2.66
Pairwise r2 <0.2	All	1	94,259	2.58	2.58	2.42	2.59	2.67	2.75
		2	94,259	2.44	2.78	2.48	2.56	2.66	2.60
	Exonica	1	26,295	2.62	2.85	2.32	3.00	2.97	3.23
		2	26,295	2.40	2.68	2.45	2.36	2.91	2.78
	Transcripta	1	52,719	2.57	2.77	2.32	2.59	2.88	2.86
		2	52,719	2.33	2.81	2.42	2.42	2.87	2.79
	Intergenic	1	41,540	2.55	2.44	2.55	2.59	2.36	2.55
		2	41,540	2.59	2.76	2.55	2.74	2.40	2.36

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

LD, linkage disequilibrium; CV, cross-validation.