the effects of the lead SNPs are more concordant across the discovery and the replication GWAS than expected by chance. We also conducted a (one-sided) binomial test to assess whether a larger fraction of the lead SNPs are significant at the 5% level in one-sided tests in the replication GWAS than expected by chance. We then followed the procedure outlined in Okbay et al. (2016)47 and conducted a Bayesian analysis to obtain estimates of the posterior distributions of the 123 SNPs’ true effect sizes (the βj ‘s), given their GWAS estimates. We used the SNPs’ estimated posterior distributions to estimate their expected replication record in the two binomial tests, and compared their actual and expected replication records.
