We estimated the extent of pleiotropy for each genome-wide associated locus from our GWAS using an Empirical Bayes approach (i.e. whether a given locus is simultaneously associated with multiple phenotypes). Using summary association statistics from a given locus as input, the method estimated the 5×5 genetic correlation of the locus and the posterior probability of association for all possible phenotype configurations, while accounting for genome-wide genetic correlations and trait residual correlations. In cases where loci associated with different phenotypes overlapped, the locus was expanded in size. Statistical details are available in the Supplementary Note, Section 3.3.
