As the ICBP has been imputed to HapMap v22, a smaller reference panel than used here for GERA, we used ImpG v1.0.156 to estimate the summary statistics for the 1000 Genomes Project reference panel SNPs used for the GERA imputation. To solve for the effect size βj of the additive coded genotype Xij (i indexing N individuals, j indexing SNPs) from the summary statistics imputed to 1000 Genomes from ImpG, we assumed that the ICBP had the same allele frequency as in the 1000 Genomes European ancestry individuals and Hardy-Weinberg Equilibrium (HWE). Let qj be the MAF, and pj=1-qj. Assuming HWE, Npj2 individuals have Xij=0, N2pjqj have Xij=1, and Nqj2 have Xij=2. It is known that SE(βj)=∑irij2/sqrt(sxx,j), where rij is the residual of the phenotype regressed on the SNP genotype Xj and sxx,j= ∑i(Xij-mean(X.j))2. It can be shown that sxx,i=2npjqj. Although ∑rij2 is unknown in ICBP, a reasonable approximation is obtained by assuming that individually each SNP explains very little of the trait variance and thus ∑rij2 is constant and does not depend on j, i.e., ∑rij2=∑ri2, and solve for
