The study defines chromatin accessibility and transcriptional landscapes in thirteen human primary blood cell types across the hematopoietic hierarchy. By exploiting the fact that enhancer landscapes better reflect cell identity than mRNA levels, the researchers enable "enhancer cytometry" to enumerate pure cell types from complex populations. They identify regulators of hematopoietic differentiation and reveal lineage ontogeny of genetic elements linked to human diseases. In acute myeloid leukemia (AML), chromatin accessibility reveals unique regulatory evolution in cancer cells with progressive mutation burden. Single AML cells exhibit distinctive mixed regulome profiles of disparate developmental stages. A method to account for regulatory heterogeneity identified cancer-specific deviations and implicated HOX factors as key regulators of pre-leukemic HSC characteristics. Regulome dynamics provide insights into hematopoietic development and disease. The study uses an optimized ATAC-seq protocol, Fast-ATAC, to profile chromatin accessibility and transcriptomes of 137 samples from 9 healthy donors and 12 AML patients, representing 16 major hematopoietic and leukemic cell types. They measure transcriptomes of 96 samples from the same donors to derive paired expression data. This reference map reveals the effects of early mutations in epigenetic modifiers and late mutations in proliferative oncogenes on leukemogenesis. Results provide key insights into the evolutionary process of leukemogenesis and identify important regulatory programs that could be targeted to disrupt this process. The study identifies regulatory networks of normal hematopoiesis, showing that specific transcription factors regulate chromatin accessibility. They find that activation of these TFs is cell-type specific, often displaying step-wise gains across developmental lineages. They also find that regulatory elements such as distal elements provide significantly improved cell-type classification compared to promoters. The study shows that regulatory heterogeneity is present in AML, with each patient-specific AML harboring a unique collection of multiple distinct normal regulatory programs. Using enhancer cytometry, they quantify the contribution of each normal cell type to each leukemic sample. They find that the majority of patient donors have AML blasts that are clonally derived and harbor all the leukemic mutations at comparable allele frequencies. The study identifies AML-specific regulatory elements and shows that synthetic normal analogs can uncover AML-specific biology. They find that the loss of HOX-mediated accessibility is the most consistent defect in pHSCs. They also find that higher pre-leukemic burden is predictive of poor overall and relapse-free survival in AML, indicating an important role for pHSCs in disease pathogenesis. The study provides a rich resource charting the epigenomic and transcriptomic landscape of 16 unique blood cell types. This resource relies on the accurate determination of regulome landscapes in primary human blood cells. The study also enriches the interpretation of GWAS results by identifying strong associations of disease-linked polymorphisms with the open chromatin landscapes of specific hematopoThe study defines chromatin accessibility and transcriptional landscapes in thirteen human primary blood cell types across the hematopoietic hierarchy. By exploiting the fact that enhancer landscapes better reflect cell identity than mRNA levels, the researchers enable "enhancer cytometry" to enumerate pure cell types from complex populations. They identify regulators of hematopoietic differentiation and reveal lineage ontogeny of genetic elements linked to human diseases. In acute myeloid leukemia (AML), chromatin accessibility reveals unique regulatory evolution in cancer cells with progressive mutation burden. Single AML cells exhibit distinctive mixed regulome profiles of disparate developmental stages. A method to account for regulatory heterogeneity identified cancer-specific deviations and implicated HOX factors as key regulators of pre-leukemic HSC characteristics. Regulome dynamics provide insights into hematopoietic development and disease. The study uses an optimized ATAC-seq protocol, Fast-ATAC, to profile chromatin accessibility and transcriptomes of 137 samples from 9 healthy donors and 12 AML patients, representing 16 major hematopoietic and leukemic cell types. They measure transcriptomes of 96 samples from the same donors to derive paired expression data. This reference map reveals the effects of early mutations in epigenetic modifiers and late mutations in proliferative oncogenes on leukemogenesis. Results provide key insights into the evolutionary process of leukemogenesis and identify important regulatory programs that could be targeted to disrupt this process. The study identifies regulatory networks of normal hematopoiesis, showing that specific transcription factors regulate chromatin accessibility. They find that activation of these TFs is cell-type specific, often displaying step-wise gains across developmental lineages. They also find that regulatory elements such as distal elements provide significantly improved cell-type classification compared to promoters. The study shows that regulatory heterogeneity is present in AML, with each patient-specific AML harboring a unique collection of multiple distinct normal regulatory programs. Using enhancer cytometry, they quantify the contribution of each normal cell type to each leukemic sample. They find that the majority of patient donors have AML blasts that are clonally derived and harbor all the leukemic mutations at comparable allele frequencies. The study identifies AML-specific regulatory elements and shows that synthetic normal analogs can uncover AML-specific biology. They find that the loss of HOX-mediated accessibility is the most consistent defect in pHSCs. They also find that higher pre-leukemic burden is predictive of poor overall and relapse-free survival in AML, indicating an important role for pHSCs in disease pathogenesis. The study provides a rich resource charting the epigenomic and transcriptomic landscape of 16 unique blood cell types. This resource relies on the accurate determination of regulome landscapes in primary human blood cells. The study also enriches the interpretation of GWAS results by identifying strong associations of disease-linked polymorphisms with the open chromatin landscapes of specific hematopo