Genetic studies in patients with autoimmune disease have identified regions of the human genome that are associated with developing disease. However, the vast majority (90%) of these regions do not fall into typical protein-coding genes, but rather into non-protein-coding stretches of the genome that are sometimes referred to as the ‘dark matter’ of the genome. The primary function of these non-protein-coding sites is to impact the expression of disease-associated genes; however, technologies to identify these sites and their connection to protein-coding genes in primary cells have been lacking. We recently developed several genome sequencing technologies that enable the measurement and interpretation of non-protein-coding DNA regions directly in patient samples, which allows us to walk this ‘last-mile’ in mapping the effects of genetic mutations on disease development in patients. In this proposal, we seek to understand this new layer of genetic information and link autoimmune disease-associated DNA elements with the cellular and molecular targets that they impact to bring about disease in patients with autoimmune disease broadly, and specifically in patients with Type 1 diabetes, systemic lupus erythematous, and multiple sclerosis. We envision that these findings will lead to new insights into the pathogenesis of autoimmunity and nominate molecular and cellular pathways that could be targeted for disease therapy.