Large-scale comparative genomics- and population genetics-based studies generate enormous amounts of polymorphism data in the form of DNA variants. The ultimate goal of these studies is to associate genetic variants with phenotypic outcomes. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an individual or population in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, population-scale genetic analyses and 3-dimensional (3D) visualisation of genotypic information encoded in Variant Call Format (VCF) on AlphaFold2 protein models. VIVID indeed offers a convenient way to rapidly assess genes of interest and accelerate research by prioritising targets for experimental validation.