Leveraging allelic imbalance in accessible chromatin to prioritize putative causal variants

Genome-wide association studies (GWASs) have uncovered many SNPs associated with complex diseases, but identifying the causal genetic variants remains very difficult. This review focuses on allele-specific chromatin accessibility (CA) variants (ASCAVs)—which are SNPs that influence CA, binding of transcription factors, and gene expression—by integrating allelic imbalance analysis with assay for transposase-accessible chromatin using sequencing (ATAC-seq) data. We discuss the underlying biological mechanisms, methodologies, and benefits of ASCAV detection by ATAC-seq, emphasizing how integrating ASCAVs with GWAS and multiomics datasets enhances the prioritization of putative causal SNPs for functional studies. By leveraging allelic imbalance in ATAC-seq, researchers can bridge the gap between GWAS signals and molecular mechanisms, advancing our understanding of gene regulation.