Evidence map›Paper›PMID 42791370›Full record

ArticleNature genetics2026

Single-cell analysis of chromatin accessibility in the human intestine identifies regulatory programs and clarifies genetic associations in Crohn's disease.

Yu Zhao, Ran Zhou, Zepeng Mu, Peter Carbonetto, Xiaoyuan Zhong, Bingqing Xie, Kaixuan Luo, Zhiwei Jiang, Jianqiao Liu, Candace M Cham and 7 more

Abstract read
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In one paragraph

Article in Nature genetics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors.

Yu Zhao *Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-2479-8438
Ran Zhou *Department of Medicine, University of Chicago, Chicago, IL, USA.
Zepeng MuCenter for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-7717-3247
Peter CarbonettoDepartment of Human Genetics, University of Chicago, Chicago, IL, USA.
Xiaoyuan ZhongDepartment of Human Genetics, University of Chicago, Chicago, IL, USA.
Bingqing XieDepartment of Medicine, University of Chicago, Chicago, IL, USA.
Kaixuan LuoDepartment of Human Genetics, University of Chicago, Chicago, IL, USA.
Zhiwei JiangDepartment of Chemistry, University of Chicago, Chicago, IL, USA.
Jianqiao LiuDepartment of Chemistry, University of Chicago, Chicago, IL, USA.
Candace M ChamDepartment of Medicine, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-7135-949X
Jason KovalDepartment of Medicine, University of Chicago, Chicago, IL, USA.
Xin HeDepartment of Human Genetics, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-9011-5212
Andrew W DahlDepartment of Medicine, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-6520-4766
Xuanyao LiuDepartment of Medicine, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-5955-6738
Eugene B ChangDepartment of Medicine, University of Chicago, Chicago, IL, USA.
Anindita BasuDepartment of Medicine, University of Chicago, Chicago, IL, USA. onibasu@uchicago.edu.ORCID http://orcid.org/0000-0001-9468-3727
Sebastian PottDepartment of Medicine, University of Chicago, Chicago, IL, USA. spott@uchicago.edu.ORCID http://orcid.org/0000-0002-4118-6150

Funding

Mechanisms and determinants of dynamic gene regulation during development and cellular differentiationR35GM142986 · NIGMS · UNIVERSITY OF CHICAGO · PI POTT, SEBASTIAN · 2021 to 2025
$2.0M
U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM142986
6 · The paper itself

Abstract

Crohn's disease is a complex inflammatory bowel disease resulting from an interplay of genetic, microbial and environmental factors. Cell-type-specific contributions to Crohn's disease etiology and genetic risk are incompletely understood. Here we built a comprehensive atlas of cell-type-resolved chromatin accessibility comprising 557,310 candidate cis-regulatory elements (cCREs) in terminal ileum and ascending colon from 23 patients with active and inactive Crohn's disease and 16 healthy controls. We identified cell-type-specific, anatomical location-specific and context-specific cCREs and characterized the regulatory programs underlying inflammatory responses in the intestinal mucosa of patients with Crohn's disease. These cell-type-resolved data confirmed that Crohn's disease heritability is primarily enriched in adaptive immune cells, in particular T cells, and in innate immune cells, including neutrophils. Using fine-mapped, noncoding Crohn's disease variants, we identified 30 variants located within cCREs. Our atlas provides a comprehensive resource to study gene-regulatory effects in Crohn's disease and health and highlights the cellular complexity underlying Crohn's disease risk.

Indexed as

ChromatinCrohn DiseaseSingle-Cell AnalysisCase-Control StudiesFemaleGenetic Predisposition to DiseaseHumansIleumIntestinal MucosaMalePolymorphism, Single NucleotideRegulatory Sequences, Nucleic AcidChromatin

Identifiers

PMID42791370

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.