{
  "abstract": ", complicating efforts to identify effector genes and relevant cell types. Here we map cis-expression quantitative trait loci (eQTLs) across 2.2 million single cells using intestinal biopsies and blood from 421 individuals, including 125 with inflammatory bowel disease (IBD). Cell-type-level eQTLs were more distal to transcription start sites, enriched in enhancers, less likely to regulate the nearest gene, and more than 3.5-fold more likely to colocalize with IBD loci detected in genome-wide association studies (GWASs) than eQTLs detected at tissue-level resolution. We nominate effector genes at more than half of known IBD loci, including MAML2, PSEN2 and ZMIZ1 in myeloid cells, implicating reduced Notch signalling in intestinal immune dysfunction. We also identify Wnt-regulated genes, including MYC, in epithelial stem and progenitor cells, suggesting that impaired renewal contributes to barrier breakdown. Our results provide a mechanistic map that links genetic risk to specific genes and cell types in IBD, and a generalized framework for interpretation of GWAS loci using single-cell eQTL mapping of disease-relevant tissues in complex diseases.",
  "abstract_shown": true,
  "affiliations": [
    "EMBL-EBI, Hinxton, UK",
    "Open Targets, Hinxton, UK",
    "Wellcome Sanger Institute, Hinxton, UK",
    "GlaxoSmithKline, Stevenage, UK",
    "Addenbrooke's Hospital, Cambridge, UK",
    "Department of Medicine, University of Cambridge, Cambridge, UK",
    "MRC Biostatistics Unit, University of Cambridge, Cambridge, UK",
    "University of Edinburgh Centre for Inflammation Research, Queens Medical Research institute, Edinburgh, UK",
    "Addenbrooke's Hospital, Cambridge, UK. tim.raine@nhs.net",
    "Open Targets, Hinxton, UK. tim.raine@nhs.net",
    "Open Targets, Hinxton, UK. ca3@sanger.ac.uk",
    "Wellcome Sanger Institute, Hinxton, UK. ca3@sanger.ac.uk"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 37,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Tobi Alegbe",
      "orcid": "0000-0003-1622-0502"
    },
    {
      "affs": [
        2
      ],
      "name": "Bradley T. Harris",
      "orcid": "0000-0001-9585-1016"
    },
    {
      "affs": [
        2
      ],
      "name": "Laura Fachal",
      "orcid": "0000-0002-7256-9752"
    },
    {
      "affs": [
        2
      ],
      "name": "Lucia Ramirez-Navarro",
      "orcid": "0000-0003-2194-2438"
    },
    {
      "affs": [
        2
      ],
      "name": "Marcus Tutert",
      "orcid": "0000-0002-4177-3371"
    },
    {
      "affs": [
        2
      ],
      "name": "Monika Krzak",
      "orcid": "0009-0005-4157-7126"
    },
    {
      "affs": [
        2
      ],
      "name": "Mennatallah Ghouraba",
      "orcid": "0000-0003-4671-3500"
    },
    {
      "affs": [
        2
      ],
      "name": "Michelle Strickland",
      "orcid": "0000-0001-8053-400X"
    },
    {
      "affs": [
        2
      ],
      "name": "Matiss Ozols",
      "orcid": "0000-0001-5663-1053"
    },
    {
      "affs": [
        2
      ],
      "name": "Céleste E. Cohen",
      "orcid": "0009-0009-8149-6127"
    },
    {
      "affs": [
        2
      ],
      "name": "Saniya Khullar",
      "orcid": "0000-0002-4166-874X"
    },
    {
      "affs": [
        2
      ],
      "name": "Eleonora Khabirova",
      "orcid": "0000-0002-5891-6789"
    },
    {
      "affs": [
        3
      ],
      "name": "Nikolaos I. Panousis",
      "orcid": "0000-0003-2890-5592"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "David Ochoa",
      "orcid": "0000-0003-1857-278X"
    },
    {
      "affs": [
        2
      ],
      "name": "Noor Wana",
      "orcid": "0009-0006-6982-1474"
    },
    {
      "affs": [
        2
      ],
      "name": "Hu Xueqi May"
    },
    {
      "affs": [
        2
      ],
      "name": "Jason Skelton"
    },
    {
      "affs": [
        2
      ],
      "name": "Jasmin Ostermayer",
      "orcid": "0000-0001-6461-398X"
    },
    {
      "affs": [
        2
      ],
      "name": "Kimberly Ai Xian Cheam",
      "orcid": "0009-0005-8842-141X"
    },
    {
      "affs": [
        2
      ],
      "name": "Dennis Leland Taylor",
      "orcid": "0000-0001-6498-6970"
    },
    {
      "affs": [
        2
      ],
      "name": "Yong Gu"
    },
    {
      "affs": [
        4
      ],
      "name": "Claire Dawson"
    },
    {
      "affs": [
        4
      ],
      "name": "Tina Thompson"
    },
    {
      "affs": [
        4
      ],
      "name": "Kenneth Arestang"
    },
    {
      "affs": [
        4
      ],
      "name": "Nilanga Nishad",
      "orcid": "0000-0002-3143-4181"
    },
    {
      "affs": [
        4
      ],
      "name": "Biljana Brezina",
      "orcid": "0000-0001-5060-5604"
    },
    {
      "affs": [
        4
      ],
      "name": "Charry Queen Caballes"
    },
    {
      "affs": [
        4
      ],
      "name": "Wendy Garri"
    },
    {
      "affs": [
        2
      ],
      "name": "Leonard Steven"
    },
    {
      "affs": [
        2
      ],
      "name": "Vivek Iyer",
      "orcid": "0000-0002-7536-0954"
    },
    {
      "affs": [
        4
      ],
      "name": "Miles Parkes",
      "orcid": "0000-0002-6467-0631"
    },
    {
      "affs": [
        5,
        6
      ],
      "name": "Chris Wallace",
      "orcid": "0000-0001-9755-1703"
    },
    {
      "affs": [
        2
      ],
      "name": "Rebecca E. McIntyre",
      "orcid": "0000-0001-5291-1533"
    },
    {
      "affs": [
        2
      ],
      "name": "Cristina Cotobal",
      "orcid": "0000-0002-5877-2228"
    },
    {
      "affs": [
        7
      ],
      "name": "Gareth‐Rhys Jones",
      "orcid": "0000-0001-7355-2357"
    },
    {
      "affs": [
        8,
        9
      ],
      "name": "Tim Raine",
      "orcid": "0000-0002-5855-9873"
    },
    {
      "affs": [
        10,
        11
      ],
      "name": "Carl A. Anderson",
      "orcid": "0000-0003-1719-7009"
    }
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  "bibtex": "https://research.draconitic.com/paper/3tdg4f854dea5.bib",
  "cited_by": 10,
  "doi": "10.1038/s41586-026-10627-z",
  "fulltext_url": null,
  "id": "3tdg4f854dea5",
  "issns": [
    "0028-0836",
    "1476-4687"
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  "landing_url": "https://doi.org/10.1038/s41586-026-10627-z",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
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  "pdf_url": null,
  "pmcid": "PMC13441992",
  "pmid": "42236949",
  "published": "2026-06-03",
  "publisher": "Nature Portfolio",
  "ris": "https://research.draconitic.com/paper/3tdg4f854dea5.ris",
  "sources": [
    {
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    {
      "field": "biology",
      "origin": "openalex:1311|Genetic Associations and Epidemiology",
      "subfield": "genetics-genomics"
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  "title": "Cell-type-resolved genetic variation shapes inflammatory bowel disease risk",
  "title_text": "Cell-type-resolved genetic variation shapes inflammatory bowel disease risk",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T13:20:49Z",
  "url": "https://research.draconitic.com/paper/3tdg4f854dea5",
  "venue": "Nature",
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