The Knowledge Portal Network is a set of interconnected, open-access web resources that aggregate, harmonize, analyze, and present genetic associations and epigenomic annotations for complex diseases, in order to help researchers elucidate the molecular details of disease mechanisms and find new therapeutic targets. It currently includes the Type 2 Diabetes (type2diabetesgenetics.org), Cardiovascular (broadcvdi.org), and Cerebrovascular (cerebrovascularportal.org) Knowledge Portals. The Portals present an analytical and computational framework whereby researchers can instantaneously search a comprehensive, up-to-date collection of association results and epigenomic annotations relevant to a particular complex disease, all seamlessly integrated with one another, and perform custom association analyses that query securely protected individual-level data.