eQTL Variants Localize to DHSs near TSSs
(A) To test the performance of GoShifter on real data, we analyzed the enrichment of 6,380 eQTLs with local DHSs at various distances (varying between 0.5 and 50 kb) to the TSS by using 10,000 random shifts. The p values for each analysis are in the top panel, and the delta-overlap measures are in the bottom panel (a higher value denotes a higher proportion of significant loci than in the null distribution).
(B) We tested enrichment of these eQTLs in various other regulatory marks (H3K9ac, H3K4me3 H3K4me1, and DHSs) associated with active transcription (10,000 random shifts) and overlap with genes and 3′ UTRs. We tested each annotation in an unstratified analysis, and we also tested for enrichment stratifying on each of the other annotations. When we tested for gene-transcript enrichment by stratifying on regulatory annotations, negative delta-overlap values indicated that eQTL SNPs were primarily captured by the regulatory annotations and depleted in gene transcripts (except for 3′ UTRs).