Table 1.

Replication of results in GERA

Discovery phenotype	Replication phenotype	# Signif genes in disc set	# Replicated genes	π1(all) in repl	π1(sig) in repl	% Replicated genes	# Replicated coloc or undeterm
Coronary artery disease	Any cardiac event	56	6	0.4%	49.1%	10.7%	6
LDL cholesterol	Dyslipidemia	282	219	5.8%	90.8%	78.5%	184
Triglycerides	Dyslipidemia	233	100	5.8%	73.1%	43.5%	69
Schizophrenia	Any psychiatric event	285	60	1.2%	47.6%	21.1%	51

Significant 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 π₁(sig) is computed using only gene-tissue pairs that were significant in the discovery set. The column ‘# replicated genes coloc or undeterm’ is the number of replicated genes excluding the ones for which there was strong evidence of independent GWAS and eQTL signals