How, where and when genes are expressed determine individual phenotypes. If gene expression is controlled by many regulatory elements, what, ultimately, controls them? And how does genetic variation affect them? The SysGenetiX project, led by the University of Geneva (UNIGE) in collaboration with the University of Lausanne (UNIL), Switzerland, sought to investigate these regulatory elements, as well as the manifold interactions between them and with genes, with the ultimate goal of understanding the mechanisms that render some people more predisposed to manifesting particular diseases than others.