We simulated quantitative phenotypes using real genotypes from European (WTCCC2) and Latino (SIGMA) data sets (see below). We fixed the proportion of causal markers at 1% and fixed SNP-heritability hg2 at 0.5, and sampled normalized effect sizes βi from a normal distribution with variance equal to hg2 divided by the number of causal markers. We calculated per-allele effect sizes bi as bi=βi2pi(1−pi), where pi is the minor allele frequency of SNP i in the European data set. We simulated phenotypes as Yj=∑i=1Mbigij+ɛj, where 𝜀j ∼ N(0, 1- hg2).
