Abstract

Widespread linkage disequilibrium and incomplete annotation of cell-to-cell state variation represent substantial challenges to elucidating mechanisms of trait-associated genetic variation. Here we perform genetic fine-mapping for blood cell traits in the UK Biobank to identify putative causal variants. These variants are enriched in genes encoding proteins in trait-relevant biological pathways and in accessible chromatin of hematopoietic progenitors. For regulatory variants, we explore patterns of developmental enhancer activity, predict molecular mechanisms, and identify likely target genes. In several instances, we localize multiple independent variants to the same regulatory element or gene. We further observe that variants with pleiotropic effects preferentially act in common progenitor populations to direct the production of distinct lineages. Finally, we leverage fine-mapped variants in conjunction with continuous epigenomic annotations to identify trait–cell type enrichments within closely related populations and in single cells. Our study provides a comprehensive framework for single-variant and single-cell analyses of genetic associations.

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Code availability

g-chromVAR is available as an open-source R package distributed freely at http://caleblareau.github.io/gchromVAR. All code required to reproduce the results discussed herein has been made available at http://github.com/caleblareau/singlecell_bloodtraits.

Data availability

All processed data are available on GitHub (https://github.com/caleblareau/singlecell_bloodtraits/). ATAC-seq profiles are available from the Gene Expression Omnibus (GEO) under accession GSE119453 and from the Sequence Read Archive (SRA) under accession PRJNA491478.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Acknowledgements

We thank members of the Sankaran, Buenrostro, and Finucane laboratories for their helpful discussions. This work was supported by National Institutes of Health (NIH) grants R01 DK103794 and R33 HL120791 (to V.G.S.), by the New York Stem Cell Foundation (NYSCF; to V.G.S.), and by the Harvard Society and Broad Institute Fellows programs (to J.D.B.). J.C.U. is supported by an NIH training grant (5T32 GM007226-43). C.A.L. is supported by an NIH predoctoral fellowship (F31 CA232670). E.L.B. is supported by the Howard Hughes Medical Institute Medical Research Fellows Program. V.G.S. is supported as an NYSCF-Robertson Investigator. This research was conducted by using the UK Biobank resource under projects 11898 and 31063.

Author information

Author notes

  1. These authors contributed equally: Jacob C. Ulirsch, Caleb A. Lareau, Erik L. Bao.

Affiliations

  1. Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA

    • Jacob C. Ulirsch
    • , Caleb A. Lareau
    • , Erik L. Bao
    • , Leif S. Ludwig
    •  & Vijay G. Sankaran
  2. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA

    • Jacob C. Ulirsch
    • , Caleb A. Lareau
    • , Erik L. Bao
    • , Leif S. Ludwig
    •  & Vijay G. Sankaran
  3. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    • Jacob C. Ulirsch
    • , Caleb A. Lareau
    • , Erik L. Bao
    • , Leif S. Ludwig
    • , Michael H. Guo
    • , Vinay K. Kartha
    • , Rany M. Salem
    • , Joel N. Hirschhorn
    • , Hilary K. Finucane
    • , Martin J. Aryee
    • , Jason D. Buenrostro
    •  & Vijay G. Sankaran
  4. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA

    • Jacob C. Ulirsch
    •  & Caleb A. Lareau
  5. Department of Pathology, Massachusetts General Hospital, Boston, MA, USA

    • Caleb A. Lareau
    •  & Martin J. Aryee
  6. Harvard–MIT Health Sciences and Technology, Harvard Medical School, Boston, MA, USA

    • Erik L. Bao
  7. Division of Endocrinology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA

    • Michael H. Guo
    • , Rany M. Salem
    •  & Joel N. Hirschhorn
  8. Department of Genetics, Harvard Medical School, Boston, MA, USA

    • Michael H. Guo
    • , Rany M. Salem
    •  & Joel N. Hirschhorn
  9. Center for Basic and Translational Obesity Research, Boston Children’s Hospital, Boston, MA, USA

    • Michael H. Guo
    • , Rany M. Salem
    •  & Joel N. Hirschhorn
  10. Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland

    • Christian Benner
  11. Department of Public Health, University of Helsinki, Helsinki, Finland

    • Christian Benner
  12. Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA

    • Ansuman T. Satpathy
  13. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA

    • Vinay K. Kartha
    •  & Jason D. Buenrostro
  14. Schmidt Fellows Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    • Hilary K. Finucane
  15. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA

    • Martin J. Aryee
  16. Harvard Stem Cell Institute, Cambridge, MA, USA

    • Vijay G. Sankaran

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Contributions

J.C.U., C.A.L., E.L.B., M.J.A., J.D.B., and V.G.S. designed the study. J.C.U., C.A.L., E.L.B., and M.H.G. analyzed data. L.S.L. performed experiments. C.B., A.T.S., V.K.K., R.M.S., and J.N.H. contributed ideas and insights. H.K.F., M.J.A., J.D.B., and V.G.S. supervised this work. J.D.B. and V.G.S. obtained funding. J.C.U., C.A.L., E.L.B., and V.G.S. wrote the manuscript with input from all authors.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Jason D. Buenrostro or Vijay G. Sankaran.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–17 and Supplementary Note

  2. Reporting Summary

  3. Supplementary Table 1

    Summary statistics and information for all fine-mapped variants with PP > 0.001

  4. Supplementary Table 2

    Summary of top fine-mapped configurations in each region

  5. Supplementary Table 3

    Summary of fine-mapped coding variants

  6. Supplementary Table 4

    Summary statistics for bulk ATAC-seq libraries

  7. Supplementary Table 5

    Summary of motif-disrupting variants occupied by corresponding transcription factors

  8. Supplementary Table 6

    Summary of putative gene targets for variants mapping to PCHi-C interactions

  9. Supplementary Table 7

    Summary of putative gene targets for variants mapping to ATAC–RNA correlations

  10. Supplementary Table 8

    Fine-mapped variants with PP > 0.05 identified in the same 3-Mb region

  11. Supplementary Table 9

    Pleiotropic variants (PP > 0.01) for blood cell count traits

  12. Supplementary Table 10

    g-chromVAR results for 39 predominantly immune-related disorders previously fine-mapped with PICS to 18 chromatin accessibility profiles

  13. Supplementary Table 11

    Application of g-chromVAR to DNase I hypersensitivity data for 53 tissues from Roadmap Epigenomics

  14. Supplementary Table 12

    Top differentially enriched transcription factors between CMP and MEP subclusters

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DOI

https://doi.org/10.1038/s41588-019-0362-6