GWAS Central began life as a joint venture between the research team of Professor Anthony Brookes in the Karolinska Institute (Sweden) and staff at Interactiva GmbH (Germany). It was first released to the public in August 1998, and called the Human Genome Bi-Allelic SEquence (HGBASE) database, with a focus solely on providing a centralized collection of known human single nucleotide polymorphisms and other simple DNA variants. One year later, the program expanded and the database structure was completely overhauled via a consortium involving the Karolinska Institute, Sweden (Anthony Brookes), the European Bioinformatics Institute, UK (Heikki Lehvaslaiho), and the European Molecular Biology Laboratory, Heidelberg (Peer Bork). Funding at that stage was provided by each of the three participating institutes, plus corporate support from Pfizer and GlaxoSmithKline. In November 2001 the project adopted the new name Human Genome Variation database (HGVbase), as this better reflected the scope of the database, its emphasis on broad data collection from many different laboratories, and its additional new role as a central depository for data collection efforts in allegiance with the Human Genome Variation Society (HGVS).

In 2004, Professor Brookes moved from the Karolinska Institute in Sweden to the University of Leicester in the UK, and in light of impressive SNP discovery efforts by the TSC and HapMap projects, HGVbase was scaled back to simply provide an alternative representation of the full marker list from dbSNP. At the same time, Professor Brookes’s team began to develop the Human Genome Variation Genotype-to-Phenotype database (HGVbaseG2P), representing the natural evolution of HGVbase into a central database for summary-level genetic association data. The work was funded by GlaxoSmithKline, the University of Leicester, and the European Community’s Sixth Framework Programme (‘INFOBIOMED’ Network of Excellence) and Seventh Framework Programme (‘GEN2PHEN’ Integrated Project). Early work in the project involved devising a powerful way of modeling phenotype and genotype- phenotype data, which itself was adopted and adapted to become the global standard ‘Phenotype And Genotype Experiment Object model’ (PaGE-OM). HGVbaseG2P then went live and replaced HGVbase in the summer of 2008, thereby extending the projects marker content to a far broader and more comprehensive range of markers (i.e., SNPs, structural variants, and STSs), along with extensive disease association findings for many alleles and genotypes.

Looking forward, HGVbaseG2P has been renamed to GWAS Central. It represents a core component of the GEN2PHEN project, intending to provide an operational model, plus free software, to help others create many similar databases across the world. These will hosted by Institutes, Consortia, and even individual laboratories, to provide those groups with a way to post their genetic association findings on the web and have them integrated into the rapidly emerging network of similar valuable resources.