Genic variants are more likely to alter gene function and affect disease risk than those that occur outside genes. Variants in genes, however, might not be sufficiently covered by the existing approaches to genome-wide association studies. Our analysis of the HapMap ENCODE data indicates that this concern is valid, and that an alternative approach that focuses on genic variants provides a more complete coverage of functionally important regions and a greater genotyping efficiency. We therefore argue that resources should be developed to make gene-centric genome-wide association studies feasible.