We display summary statistics for this replication analysis in Table 1. Among the 56 genes significantly associated with CAD in the discovery set, 6 (11%) were significantly associated with “Any cardiac event” in GERA. Using “Dyslipidemia” as the closest matching phenotype, 78.5% and 43.5% of LDL and triglyceride genes replicated, respectively. Among the 285 genes associated with schizophrenia in the discovery set, 51 (21%) replicated. The low replication rate for CAD and Schizophrenia is likely due to the broad phenotype definitions in the replication.Table 1Replication of results in GERADiscovery phenotypeReplication phenotype# Signif genes in disc set# Replicated genesπ1(all) in replπ1(sig) in repl% Replicated genes# Replicated coloc or undetermCoronary artery diseaseAny cardiac event5660.4%49.1%10.7%6LDL cholesterolDyslipidemia2822195.8%90.8%78.5%184TriglyceridesDyslipidemia2331005.8%73.1%43.5%69SchizophreniaAny psychiatric event285601.2%47.6%21.1%51Significant genes/tissue pairs were replicated using a closely matched phenotype in an independent dataset from the GERA cohort36. The criteria consisted in significance threshold for replication at p < 0.05, concordant directions of effect, and meta analysis p-value less than the Bonferroni threshold in the discovery set. π1 is an estimate of proportion of true positives in the replication set. π1(all) uses all gene–tissue pairs whereas
