Genome-wide characterization of molecular and cellular effects of genetic variants is essential for understanding biological processes that underlie genetic associations to disease. This can be pursued by many approaches: population genetic approaches that associate genetic variation to molecular phenotypes, large-scale CRISPR perturbations coupled with single-cell readouts, and predictive models of variant effects. Our work shows how complementary insights from joint application of multiple tools uncovers functional genetic architecture of human traits. This has applications both for fundamental understanding of genome biology, mechanisms underlying human disease, and future applications in precision medicine.