Using similar techniques to derive isoform expression quantitative trait loci (isoQTLs), we identified 3,355,111 significant cis-isoQTLs at FDR ≤ 5%, representing 27,691 isoforms of 10,779 genes. IsoQTLs and gene-level eQTLs overlapped substantially; 58% of isoQTLs were cis-eQTLs for the parent gene at FDR ≤ 5%; conversely, 71% of cis-eQTLs for genes with at least one represented isoform were isoQTLs at FDR ≤ 5%. There were, however, 1,584 genes having no cis-eQTL (FDR ≤ 5%) that nevertheless had at least one significant isoQTL. At the isoform level, there were 39,414 significant trans-isoQTLs, representing 964 isoforms (836 genes), of which 61% were also trans-eQTLs for the same gene.
