The Genome Variation Map (GVM) is a public data repository of genome variations, including single nucleotide polymorphisms (SNP) and small insertions and deletions (INDEL), with particular focuses on human as well as cultivated plants and domesticated animals. GVM collects, integrates and visualizes genome variations for a wide variety of species, accepts submissions of different types of genome variations from all over the world and provides open access for all publicly available data. Based on a large collection of raw sequence data from public repositories, GVM integrates a large number of genome variants for a number of species and provides web interfaces for data submission, search, browse and visualization.