Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation
Local-eQTL for Pik3c2g were detected in all three tissues in the 3Mb region surrounding its TSS. The genomes of the CC founders can be simplified in terms of contributions from three subspecies lineages of M. musculus: dom (blue), cast (yellow), and mus (red). The effects of each local-eQTL matched the subspecies contributions near the eQTL coordinates, with low expressing subspecies alleles colored teal and high expressing alleles colored salmon, consistent with local-eQTL for Pik3c2g being distinct and tissue-specific. The gene expression data are represented as interquartile range bars, categorized based on most likely diplotype at the eQTL for each CC strain. Haplotype and variants associations are included for each tissue, with the red tick representing the Pik3c2g TSS, black ticks representing variant association peak, and colored ticks representing the haplotype association peak. The most rigorous procedure to detect each QTL (Analysis L, C, or G) is reported. Haplotype effects, estimated as constrained BLUPs, were consistent with the expression data, and uncorrelated across the tissues.