The architecture of allele-specific regulatory variant effects across five human genomes

The overwhelming majority of genetic associations with complex traits and disease involve non-coding genetic variants. Those variants are substantially enriched in gene regulatory elements, indicating that allelic impacts on gene regulatory element activity is a major contributor to those associations. As a step towards fine mapping the mechanisms within those associations, several studies have identified variants associated with gene expression and chromatin accessibility within those phenotypic associations. However, connecting those associations with functional impacts on gene regulatory element activity remains a major challenge. Here, we functionally measured allele-specific regulatory element activity across five human genomes using the genome-wide reporter assay STARR-seq. We identified tens of thousands of gene regulatory elements and estimated allele effects at ∼200,000 genetic variants therein, including ∼10,000 indels in our study population. Allelic effects on regulatory element activity correspond closely with predicted impacts on transcription factor binding motifs. The measured variant effects also allow us to fine map potential causal variants within eQTLs and chromatin QTLs from the same population. Together, these results provide an initial atlas of genome-wide variant effects across the human genome and demonstrate the potential for such approaches to prioritize causal variants for future mechanistic investigation.