Genome-wide association studies (GWAS) have identified many noncoding variants associated with common diseases and traits. We show that these variants are concentrated in regulatory DNA marked by DNase I hypersensitive sites (DHSs). 88% of such DHSs are active during fetal development, and are enriched for gestational exposure-related phenotypes. We identify distant gene targets for hundreds of DHSs that may explain phenotype associations. Disease-associated variants systematically perturb transcription factor recognition sequences, frequently alter allelic chromatin states, and form regulatory networks. We also demonstrate tissue-selective enrichment of more weakly disease-associated variants within DHSs, and the de novo identification of pathogenic cell types for Crohn’s disease, multiple sclerosis, and an electrocardiogram trait, without prior knowledge of physiological mechanisms. Our results suggest pervasive involvement of regulatory DNA variation in common human disease, and provide pathogenic insights into diverse disorders.

Role of funding source: Personnel from Juno Therapeutics reviewed the draft manuscript and assisted with statistical analyses but were not involved in recruitment or clinical care of participants, performance of response assessments, or conduct of laboratory assays. Personnel from the other funding sources did not contribute to the design, conduct, or analysis of the study.

Mouse bone marrow hematopoietic stem cells were isolated with the use of a variety of phenotypic markers. These cells can proliferate and differentiate with approximately unit efficiency into myelomonocytic cells, B cells, or T cells. Thirty of these cells are sufficient to save 50 percent of lethally irradiated mice, and to reconstitute all blood cell types in the survivors.