We estimated the GRM of all individuals in the combined data from all the autosomal SNPs using the method we recently developed4,10, and excluded one of each pair of individuals with an estimated genetic relationship > 0.025. We then estimated the variance explained by all autosomal SNPs by restricted maximum likelihood analysis of an MLM y = Xβ + gG + ε, where y is a vector of phenotypes, β is a vector of fixed effects (e.g. the first 10 PCs) with its incidence matrix of X, gG is a vector of aggregate effects of all autosomal SNPs with var(gG)=AGσG2 and AG is the GRM estimated from all autosomal SNPs. The proportion of variance explained by all autosomal SNPs is defined as hG2=σG2/σP2 with σP2 being the phenotypic variance.
