Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease
Lei Hou, Xushen Xiong, Yongjin Park, Carles A. Boix, Benjamin T. James, Na Sun, Liang He, Aman Patel, Zhizhuo Zhang, Benoit Molinié, Nicholas Van Wittenberghe, Scott Steelman, Chad Nusbaum, François Aguet, Kristin Ardlie, Manolis Kellis
Abstract
Genetic variants associated with complex traits are primarily noncoding, and their effects on gene-regulatory activity remain largely uncharacterized. To address this, we profile epigenomic variation of histone mark H3K27ac across 387 brain, heart, muscle and lung samples from Genotype-Tissue Expression (GTEx). We annotate 282 k active regulatory elements (AREs) with tissue-specific activity patterns. We identify 2,436 sex-biased AREs and 5,397 genetically influenced AREs associated with 130 k genetic variants (haQTLs) across tissues. We integrate genetic and epigenomic variation to provide mechanistic insights for disease-associated loci from 55 genome-wide association studies (GWAS), by revealing candidate tissues of action, driver SNPs and impacted AREs. Lastly, we build ARE-gene linking scores based on genetics (gLink scores) and demonstrate their unique ability to prioritize SNP-ARE-gene circuits. Overall, our epigenomic datasets, computational integration and mechanistic predictions provide valuable resources and important insights for understanding the molecular basis of human diseases/traits such as schizophrenia.