Approaches that combine expression quantitative trait loci (eQTLs) and genome-wide association (GWA) studies are offering new functional information about the aetiology of complex human traits and diseases. Improved study designs--which take into account technological advances in resolving the transcriptome, cell history and state, population of origin and diverse endophenotypes--are providing insights into the architecture of disease and the landscape of gene regulation in humans. Furthermore, these advances are helping to establish links between cellular effects and organismal traits.