We identified 7 unique pairs of unlinked SNPs that are associated with the same phenotype and that also affect the same downstream genes in trans or cis (at FDR 0.05, Table 2, Figure 4a). In order to establish whether this was more than expected by chance, we repeated this analysis, while using a set of trans-eQTLs, equal in size to the set of real trans-eQTLs, most significant after having permuted the expression sample identifiers. We performed this procedure 100 times, and observed on average only 0.15 unique pairs of unlinked SNPs (range [0, 3], Figure 4b) that showed this convergence, which indicates that the observed number of converging pairs of SNPs is 47 times more than expected (EVD p<1.0×10−16) and implies a false-positive rate of 0.021.
