ABSTRACT Thousands of genetic loci are associated with human traits or disease risk, and these loci each typically contain tens to hundreds of variants, most of which are non-coding and lack direct evidence of effects on genes. Experimental tests of genomic variants are needed to identify functional effects, which can be specific to one sex, tissue, and/or perturbed environmental context. Testing effects of risk variants on gene regulation requires an ability to quantify the potentially modest consequences of thousands of alleles in a carefully controlled study. Our overarching goal is to systematically characterize the impact of human genetic variation on gene regulation via massively parallel reporter assays (MPRA). We will select variants based primarily on genome-wide association studies (GWAS) for common diseases and complex traits relevant to the brain, liver, lung, muscle, and/or heart. We will examine all plausible functional candidates at prioritized GWAS loci to provide data for tests of regulatory variant prediction algorithms, positive control variants, and variants prioritized based on regulatory element annotations. The gene regulatory effect of ~500,000 variant alleles will be interrogated in five organs (brain, liver, lung, muscle and heart) using systemic circulation of adeno-associated viral (AAV) MPRA libraries. We will repeat this experiment in a perturbed inflammatory state to evaluate gene-environment interactions. As a result, we will comprehensively characterize variant effects on regulatory function by analyses of variants in the physiological conditions of multiple tissues, in both sexes, with and without perturbation typical of disease environments. Selected variants will be edited into human pluripotent cells for validation. As members of the Impact of Genomic Variation on Function (IGVF) Consortium, we will generate a regulatory variant catalog for the community, and enable future studies through data collection and predictive models. Successful completion of these aims will provide ~10 million allelic effect data points that encompass tissue-, sex-, and perturbation- specific regulatory effects. We will work with the IGVF consortium to finalize selection of variants, organs, and perturbations to generate a comprehensive catalog. The expertise of the study investigators in GWAS, statistical and computational genetics, human genomics, AAV delivery, and mouse physiology make achievement of these aims feasible and likely highly informative to understand how genomic variation impacts human health and disease.

PUBLIC HEALTH RELEVANCE Thousands of DNA variants may contribute to common diseases by affecting how well a gene is expressed, but the identity of these variants is unknown. The proposed study will identify specific DNA variants that alter gene expression level to influence risk of disease. The study will determine whether variants act differently in males and females; in the brain, liver, muscle, lung, and heart; and in or out of an inflamed environment. The results may lead to identification of new targets for drugs to treat common diseases.