. Author manuscript; available in PMC: 2015 May 1.

Published in final edited form as: Nat Genet. 2014 Oct 5;46(11):1173–1186. doi: 10.1038/ng.3097

Table 1. Estimates of variance explained by SNPs selected at different significance levels.

The SNPs were selected by an approximate conditional and joint multiple-SNP analysis (GCTA-COJO) of the summary statistics from the meta-analysis. The target cohort for variance estimation was excluded from the meta-analysis.

Threshold	QIMR (n = 3,924)			FRAM (n = 1,145)			TwinGene (n = 5,668)			WTCCC-T2D (n = 1,914)			B-PROOF(n = 2,555)			^a Weighted average		^b Pred.

	#SNP	h²_g	SE	#SNP	h²_g	SE	#SNP	h²_g	SE	#SNP	h²_g	SE	#SNP	h²_g	SE	h²_g	SE	h²_g
5E-8	675	0.164	0.016	656	0.190	0.040	670	0.159	0.013	679	0.143	0.025	691	0.152	0.021	0.159	0.008	0.149
5E-7	887	0.187	0.017	862	0.210	0.045	866	0.170	0.013	890	0.184	0.028	886	0.162	0.022	0.176	0.009	0.166
5E-6	1245	0.196	0.018	1202	0.207	0.050	1186	0.188	0.014	1256	0.201	0.030	1232	0.175	0.024	0.190	0.009	0.186
5E-5	1950	0.212	0.020	1891	0.183	0.060	1918	0.208	0.015	1985	0.208	0.037	1947	0.194	0.029	0.206	0.010	0.218
5E-4	3754	0.248	0.024	3671	0.239	0.080	3689	0.239	0.017	3771	0.201	0.047	3661	0.248	0.037	0.240	0.013	0.259
5E-3	9693	0.297	0.035	9403	0.171	0.126	9548	0.287	0.025	9677	0.267	0.070	9174	0.341	0.055	0.292	0.018	0.339
^cHM3	1.08M	0.473	0.086	1.06M	0.313	0.291	1.12M	0.522	0.060	0.97M	0.534	0.170	1.09M	0.463	0.126	0.498	0.044

The estimates from all the five cohorts were averaged by the inverse-variance approach i.e. Σ_i (h²_g(_i₎/SE²_i)/Σ_i (1/SE²_i);

the predicted variance explained by the selected SNPs (V_g) from the within-family prediction analysis;

SNPs from HapMap3 project¹¹.