Figure 4c shows that the COLOC-estimated proportion of non-colocalized (independent) GWAS and eQTL signals is larger among TWAS significant genes than among S-PrediXcan significant ones. We believe this is due to the polygenic component of BSLMM models, a wider set of SNPs increasing the chances of COLOC yielding a non-colocalized result. Figure 4d shows that, for most traits, the COLOC-estimated proportion of colocalized signals is larger among S-PrediXcan significant genes than S-TWAS significant genes.
