Several steps are needed to incorporate individual SNP effects into Genomic SEM. The first step requires that the inputted genetic covariance matrix be expanded to include covariances between the SNP and each of the phenotypes, g1 through gk, by appending a vector of SNP-phenotype covariances (SSNP) to SLDSC: SFull=[σSNP2σSNP,g1h12σSNP,g2σg1,g2h22σSNP,g3σg1,g3σg2,g3h32⋮⋮⋱σSNP,gkσg1,gkσg2,gkσg3,gk⋯hk2]
