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Genome-wide studies on the genetic basis of gene expression have advanced considerably our understanding of the function of the human genome. Large collections of expression quantitative trait loci (i.e., genetic variations affecting gene expression; eQTLs) are now available across many cell types, tissues, and conditions and are commonly used to better interpret the effects of noncoding genetic variations. Although this constitutes an extraordinary resource to study complex organismal traits and diseases, we still have a poor understanding of how they affect the regulatory machinery, which regulatory elements (REs) they perturb, and how their effects propagate along regulatory interactions.

In this study, we aimed to characterize the complex and cell type–specific interplay between genetic variation, REs, and gene expression to dissect cis- and trans-regulatory coordination. To …