In order to validate the key statistical properties of Stratified Genomic SEM, we began by simulating genetically correlated phenotypes that were enriched in six annotations. We then show that our multivariate extension of S-LDSC produces accurate estimates of stratified genetic covariance along with unbiased standard errors (Supplementary Figs. 8-10 and Supplementary Tables 7-9). Finally, we demonstrate that these stratified genetic covariance matrices can be used as input to Stratified Genomic SEM to produce unbiased factor loadings and unbiased standard errors (Supplementary Fig. 11).
