GWAS Central is built upon a basal layer of Markers that comprises all known SNPs and other variants from public databases such as dbSNP and the DBGV.

Genetic association significance findings are added on top of the Marker data, and organised the same way that investigations are reported in typical journal manuscripts. Critically, no individual level genotypes or phenotypes are presented in GWAS Central – only group level aggregated (summary level) data.

The largest unit in a data submission is a Study, which can be thought of as being equivalent to one journal article. This may contain one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. Sample Panels may be characterised in terms of various Phenotypes, and they also may be combined and/or split into Assayed Panels. The Assayed Panels are used as the basis for reporting genetic association findings (in ‘Analysis Experiments’). Environmental factors are handled as part of the Sample Panel and Assayed Panel data structures.