Here we describe MyGene2, Geno2MP, VariantMatcher, and Franklin; databases that have made variant-level information together with phenotype or phenotypic features available to researchers, clinicians, health care providers and patients. Following in the footsteps of the Matchmaker Exchange project that connects exome, genome, and phenotype databases at the gene level, these databases plan to connect to each other using Data Connect, a standard for discovery and search of biomedical data from the Global Alliance for Genomics and Health (GA4GH).