Figure 5b compares S-PrediXcan (elastic net) and SMR association results. As expected, SMR p-values tend to be less significant than S-PrediXcan’s in large part due to the additional adjustment for the uncertainty in the eQTL association. Figure 5c, d show that the SMR significance is bounded by the eQTL and GWAS association strengths of the top eQTL. Figure 5g shows a comparison between SMR’s and S-PrediXcan’s proportion of non-colocalization, while Fig. 5h compares proportion of colocalization, as estimated by COLOC. SMR shows a higher proportion of colocalized and independent signals. This is expected since SMR uses a more stringent eQTL association criterion so that there are few significant genes in the undetermined region.
