Phenotypes were subsequently constructed as the weighted linear combination of one of the six “total” genotypes and domain-specific environmental factors (randomly sampled from a normal distribution with M = 0, SD = 1). Heritabilities for phenotypes 1-6 were all set to hk2=60%, such that the weights for the genotypes were hk2 and the weights for the environmental factors were (1−hk2). Each of the 600 phenotypes (100 sets of 6 phenotypes) was then analyzed as a univariate GWAS in PLINK55 to produce univariate GWAS summary statistics. The summary statistics were then munged, and Stratified Genomic SEM using the 1000 Genomes Phase 3 BaselineLD Version 2.2 model was used to construct 100 sets of 6 × 6 stratified zero-order genetic covariance matrices (S0), τ covariance matrices (Sτ), and their corresponding sampling covariance matrices (VS0 and VSτ).
