We simulated quantitative traits under an infinitesimal model in 2062 controls from a Swedish study. To simulate the standard scenario where many causal SNPs are not genotyped, we simulated phenotypes by drawing causal SNPs from 622,146 best-guess imputed 1000 Genomes SNPs on chromosome 2, then retained only the 90,980 HM3 SNPs with MAF above 5% for LD Score regression.
