To compare H-MAGMA with eQTL-based tools, we used previously reported schizophrenia (SCZ) risk genes obtained through the transcriptome-wide association study (TWAS)40 and coloc3. Both TWAS and coloc were performed on SCZ GWAS52 using the largest eQTL resource obtained from the adult human DLPFC3. We restricted our H-MAGMA results to those derived from the adult brain so that we can match the developmental period (adult) and brain region (DLPFC) with the eQTL database. TWAS identified 708 SCZ-associated genes (TWAS SCZ genes) whose imputed expression values are correlated with SCZ (FDR<0.05). Coloc identified 255 SCZ-associated genes (coloc SCZ genes) whose eQTLs co-localize with SCZ genome-wide significant (GWS) loci (PP4>(PP0+PP1+PP2+PP3)).
