Farh, Kyle Kai-HowMarson, AlexanderZhu, JiangKleinewietfeld, MarkusHousley, William J.Beik, SamanthaShoresh, NoamWhitton, HollyRyan, Russell J.H.Shishkin, Alexander A.Hatan, MeitalCarrasco-Alfonso, Marlene J.Mayer, DitaLuckey, C. JohnPatsopoulos, NikolaosDe Jager, PhilipKuchroo, VijayEpstein, Charles BDaly, MarkHafler, DavidBernstein, Bradley2015-09-012014Farh, K. K., A. Marson, J. Zhu, M. Kleinewietfeld, W. J. Housley, S. Beik, N. Shoresh, et al. 2014. “Genetic and Epigenetic Fine-Mapping of Causal Autoimmune Disease Variants.” Nature 518 (7539): 337-343. doi:10.1038/nature13835. http://dx.doi.org/10.1038/nature13835.0028-0836http://nrs.harvard.edu/urn-3:HUL.InstRepos:21462636Summary Genome-wide association studies have identified loci underlying human diseases, but the causal nucleotide changes and mechanisms remain largely unknown. Here we developed a fine-mapping algorithm to identify candidate causal variants for 21 autoimmune diseases from genotyping data. We integrated these predictions with transcription and cis-regulatory element annotations, derived by mapping RNA and chromatin in primary immune cells, including resting and stimulated CD4+ T-cell subsets, regulatory T-cells, CD8+ T-cells, B-cells, and monocytes. We find that ~90% of causal variants are noncoding, with ~60% mapping to immune-cell enhancers, many of which gain histone acetylation and transcribe enhancer-associated RNA upon immune stimulation. Causal variants tend to occur near binding sites for master regulators of immune differentiation and stimulus-dependent gene activation, but only 10–20% directly alter recognizable transcription factor binding motifs. Rather, most noncoding risk variants, including those that alter gene expression, affect non-canonical sequence determinants not well-explained by current gene regulatory models.en-USJournal Article2015-09-0110.1038/nature13835