Per trait we assessed all the SNPs that have been reported to be associated with that particular trait. We analyzed per trait all possible SNP-pairs. If a pair of SNPs was not in LD (r2<0.001) we assessed whether they affected the same gene in cis or trans. When using the trait-associated cis- and trans-eQTLs that had been identified when controlling the FDR at 0.05, we identified 7 unique pairs of SNPs that caused both the same phenotype and also affected the same gene(s). When using a somewhat more relaxed set of trans-eQTLs, identified when controlling the FDR at 0.5, we identified 18 unique pairs of SNPs that affect the same downstream gene.
