For piRNA enrichment analysis, we obtained a list of 6,250 piRNA clusters that were experimentally determined from RNA sequencing of human testis34. When considering all unique trans-eVariants identified in all tissues, we identified an enrichment of trans-eQTLs overlapping a piRNA cluster (17.8%) compared to the null expectation that trans-eVariants are randomly distributed relative to piRNA clusters (2.5%). To further establish the statistical significance of this observation, we generated a null distribution of piRNA-eVariant overlap by permutation. Using bedtools277, we permuted the location of piRNA clusters on the human genome 10,000 times, requiring the piRNA clusters to be excluded from centromeres and sex chromosomes. We also evaluated the proportion of trans-eVariants located within 10 kb of a piRNA cluster, and estimated the significance of this enrichment using the same permutation scheme.
