The recent application of high throughput genotyping in humans has yielded numerous insights into the genetic basis of human phenotypes and unprecedented amount of genetic variation data. Each genome wide significant finding has explained only a tiny proportion of phenotypic variation, yet genome wide association studies (GWAS) in their entirety can provide unprecedented windows into the molecular genetics of these phenotypes. New methods are emerging to mine modest association signals from these data using information on biological pathways and networks underlying the phenotype variation. These methods promise to enhance the information extracted from GWAS providing grounds for follow up studies of both a genetic and molecular nature.