Genetic variants shape single-cell chromatin accessibility and disease risk
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T cells. A graph neural network trained on both eQTL and caQTL layers inferred peak-gene links in unpaired multiome data with up to 17.2% higher accuracy than QTL-agnostic data, uncovering 128 additional transcription factor-target pairs (22% increase). Together, these results show that genetic variants shape chromatin accessibility in a cell-type-specific and cell-state-specific manner, influencing immune function and disease risk.
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GC-Content Normalization for RNA-Seq Data
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SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
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Systematic mapping of functional enhancer–promoter connections with CRISPR interference
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- Authors
- Xue, A., Fan, J., Dong, O. A., Huang, H. L., Chen, L., Allen, P. C., Spenceley, E., Sagi-Zsigmond, E., Bowen, B., Henry, A., Cuomo, A. S. E., Tanudisastro, H. A., Qiao, Z., Dorans, E., Ben-David, E., Farh, K. K.-H., Hu, L., Liu, Y. C., Neavin, D. R., Lee, A. S., Senabouth, A., Bartie, C., McCloy, R. A., Chin, V., Zhou, W., Price, A. L., de Lange, K. M., Figtree, G. A., Hewitt, A. W., MacArthur, D. G., & Powell, J. E.
- Affiliations
- Garvan Institute of Medical Research (AU)
- The University of Sydney (AU)
- Illumina (United States) (US)
- Broad Institute (US)
- University of Tasmania (AU)
- ORCID
- Xue, Angli
- Dong, Oscar A.
- Huang, Hao Lawrence
- Chen, Ling
- Allen, Peter C.
- Spenceley, Eleanor
- Sagi-Zsigmond, Eszter
- Henry, Albert
- Cuomo, Anna S. E.
- Tanudisastro, Hope A.
- Dorans, Elizabeth
- Ben-David, Eyal
- Farh, Kyle Kai-How
- Liu, Yijia Christiana
- Neavin, Drew R.
- Lee, Arthur S.
- Senabouth, Anne
- McCloy, Rachael A.
- Chin, Venessa
- Zhou, Wei
- Price, Alkes L.
- Hewitt, Alex W.
- MacArthur, Daniel G.
- Powell, Joseph E.
- Venue
- Nature
- Published
- 2026-10-28
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W7224084810
- Cited by
- 3
- References
- 8
- Citations by year
- 2026: 3
- FWCI
- 6.20
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- genetic variants, single-cell chromatin accessibility, chromatin accessibility, disease risk, single-cell genomics, epigenetics
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