%0 Journal Article %A Michael Guo %A Satish K. Nandakumar %A Jacob C. Ulirsch %A Seyedeh Maryam Zekavat %A Jason D. Buenrostro %A Pradeep Natarajan %A Rany Salem %A Roberto Chiarle %A Mario Mitt %A Mart Kals %A Kalle Pärn %A Krista Fischer %A Lili Milani %A Reedik Mägi %A Priit Palta %A Stacey B. Gabriel %A Andres Metspalu %A Eric S. Lander %A Sekar Kathiresan %A Joel N. Hirschhorn %A Tõnu Esko %A Vijay G. Sankaran %T Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms %D 2016 %R 10.1101/067934 %J bioRxiv %P 067934 %X Genetic variants affecting hematopoiesis can influence commonly measured blood cell traits. To identify factors that affect hematopoiesis, we performed association studies for blood cell traits in the population-based Estonian Biobank using high coverage whole genome sequencing (WGS) in 2,284 samples and SNP genotyping in an additional ~17,000 samples. Our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic data sets provided evidence for causal mechanisms at several loci, including at a novel basophil count-associated locus near the master hematopoietic transcription factor CEBPA. The fine-mapped variant at this basophil count association near CEBPA overlapped an enhancer active in common myeloid progenitors and influenced its activity. In situ perturbation of this enhancer by CRISPR/Cas9 mutagenesis in hematopoietic stem and progenitor cells demonstrated that it is necessary for and specifically regulates CEBPA expression during basophil differentiation. We additionally identified basophil count-associated variation at another more pleiotropic myeloid enhancer near GATA2, highlighting regulatory mechanisms for ordered expression of master hematopoietic regulators during lineage specification. Our study illustrates how population-based genetic studies can provide key insights into poorly understood cell differentiation processes of considerable physiologic relevance. %U https://www.biorxiv.org/content/biorxiv/early/2016/08/04/067934.full.pdf