The contribution of cis-regulatory mutations to human disease remains poorly understood. Whole-genome sequencing can identify all noncoding variants, yet the discrimination of causal regulatory mutations represents a formidable challenge. We used epigenomic annotation in human embryonic stem cell (hESC)-derived pancreatic progenitor cells to guide the interpretation of whole-genome sequences from individuals with isolated pancreatic agenesis. This analysis uncovered six different recessive mutations in a previously uncharacterized ∼400-bp sequence located 25 kb downstream of PTF1A (encoding pancreas-specific transcription factor 1a) in ten families with pancreatic agenesis. We show that this region acts as a developmental enhancer of PTF1A and that the mutations abolish enhancer activity. These mutations are the most common cause of isolated pancreatic agenesis. Integrating genome sequencing and epigenomic annotation in a disease-relevant cell type can thus uncover new noncoding elements underlying human development and disease. Fil: Weedon, M. N.. University of Exeter; Reino Unido Fil: Cebola, I.. Institut d’Investigacions Biomèdiques August Pi i Sunyer; España. Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas; España. Imperial College London; Reino Unido Fil: Patch, A. M.. University of Exeter; Reino Unido Fil: Flanagan, S.. University of Exeter; Reino Unido Fil: De Franco, E.. University of Exeter; Reino Unido Fil: Caswell, R.. University of Exeter; Reino Unido Fil: Rodríguez Seguí, Santiago Andrés. Institut d’Investigacions Biomèdiques August Pi i Sunyer; España. Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas; España. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Shaw Smith, C.. University of Exeter; Reino Unido Fil: Cho, C.. Anne McLaren Laboratory for Regenerative Medicine; Reino Unido Fil: Allen, H. L.. University of Exeter; Reino Unido Fil: Houghton, J.. University of Exeter; Reino Unido Fil: Roth, C. L.. Seattle Children’s Hospital Research Institute; Estados Unidos Fil: Chen, R.. King’s College London; Reino Unido Fil: Hussain, K.. University College London; Reino Unido Fil: Marsh, P.. King’s College London; Reino Unido Fil: Vallier, L.. Anne McLaren Laboratory for Regenerative Medicine; Reino Unido Fil: Murray, A.. University of Exeter; Reino Unido Fil: International Pancreatic Agenesis Consortium. No especifica; Fil: Ellard, S.. University of Exeter; Reino Unido Fil: Ferrer, J.. Institut d’Investigacions Biomèdiques August Pi i Sunyer; España. Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas; España. Imperial College London; Reino Unido Fil: Hattersley, A. T.. University of Exeter; Reino Unido