We determined which unlinked trait-associated SNPs show eQTL effects on exactly the same gene: per trait, we analyzed the SNPs that are known to be associated with this trait and assessed whether any unlinked SNP pair (r2 < 0.2, distance between SNPs > 5Mb) showed a cis- and/or trans-eQTL effect on exactly the same gene, as previously described5. To determine whether the number of traits for which we observed this phenomenon was higher than expected by chance, we re-ran this analysis 20 times, each time using a different set of permuted trans-eQTLs, equal in size to the non-permuted set of trans-eQTLs.
