While H-MAGMA uses the whole genome as genetic background, coloc and TWAS require a more carefully defined background. Because coloc is a GWS loci-centric approach, e-genes within GWS loci ± 1Mb were considered as background (3,632 genes). On the other hand, TWAS is a genome-wide approach and uses cis-heritable genes as background (13,396 genes). We therefore intersected H-MAGMA SCZ association results with coloc and TWAS background, from which 1,576 and 2,801 H-MAGMA SCZ genes (FDR<0.05) were selected and compared with coloc and TWAS SCZ genes, respectively. By comparing H-MAGMA SCZ genes and coloc/TWAS SCZ genes, we obtained 3,004 H-MAGMA selective genes (genes identified by H-MAGMA but not by TWAS and/or coloc). SNPs mapped to H-MAGMA selective genes were subsequently identified via H-MAGMA input file from the adult brain (H-MAGMA SNPs). Finally, heritability enrichment of H-MAGMA SNPs was calculated by S-LDSC to demonstrate that H-MAGMA genes without eQTL support still explain a significant proportion of heritability.
