ArticleNature2026
An encyclopedia of human enhancer-gene regulatory interactions.
Abstract read
In one paragraph
Article in Nature, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
26citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-Phenotype Genome-Wide Association Study on the Shared Genetic Susceptibility to Systemic Sclerosis and Primary Biliary Cholangitis.Arthritis & rheumatology (Hoboken, N.J.) · 2025Pooled it
- Mapping enhancer-gene regulatory interactions from single-cell data.Nature genetics · 2026Article
- Positive selection on brain cis-regulatory elements in the human lineage drives changes in gene expression and susceptibility to neuropsychiatric disorders.HGG advances · 2026Article
- Buffering of gene dosage response curves for human complex traits.Cell genomics · 2026Article
- Metadomain and metaloop genome interactions in mammalian T cells.Cell reports · 2026Article
- A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia.bioRxiv : the preprint server for biology · 2026Article
- An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia.bioRxiv : the preprint server for biology · 2026Article
- Type 2 Diabetes and Obesity Alter Exercise Training-Induced Transcriptional Adaptations to Subcutaneous White Adipose Tissue.bioRxiv : the preprint server for biology · 2025Article
- Article
- Discovery of NANOG enhancers and their essential roles in self-renewal and differentiation in human embryonic stem cells.Stem cell reports · 2025Article
- Characterization of non-coding variants associated with transcription-factor binding through ATAC-seq-defined footprint QTLs in liver.American journal of human genetics · 2025Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.bioRxiv : the preprint server for biology · 2025Article
- Quantifying the influence of genetic context on duplicated mammalian genes.bioRxiv : the preprint server for biology · 2025Article
- A replication study of novel fetal hemoglobin-associated genetic variants in sickle cell disease-only cohorts.Human molecular genetics · 2025Article
- Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes.Science (New York, N.Y.) · 2025Article
- Three-dimensional regulatory hubs support oncogenic programs in glioblastoma.Molecular cell · 2025Article
- Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations.Cell genomics · 2025Article
- Article
- GENCODE 2025: reference gene annotation for human and mouse.Nucleic acids research · 2025Article
- Understanding genetic variants in context.eLife · 2024Article
Corrections and comments
- Update of
Authors and funding
46 authors.
Andreas R Gschwind *Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-0769-6907
Kristy S Mualim *Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-6898-3205
Alireza Karbalayghareh *Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-4308-2582
Maya U Sheth *Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Kushal K Dey *Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
Evelyn Jagoda *The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ramil N Nurtdinov *Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.ORCID http://orcid.org/0000-0002-9753-6287
Wang Xi *Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Anthony S TanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
James GalanteDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-9289-3090
Hank JonesDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0009-0007-3220-3098
X Rosa MaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-8297-4279
David YaoDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-2232-524X
Dulguun AmgalanDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Judhajeet RayThe Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-1524-2603
Chad J MungerDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Joseph NasserBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Žiga AvsecGoogle DeepMind, London, UK.ORCID http://orcid.org/0000-0003-3119-0567
Benjamin T JamesBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6228-055X
Muhammad S ShamimDepartment of Pathology, Mass General Brigham, Boston, MA, USA.ORCID http://orcid.org/0000-0002-2600-5147
Neva C DurandGene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0009-0006-5647-2623
Suhas S P RaoDepartment of Medicine, University of California San Francisco, San Francisco, CA, USA.
Ragini MahajanCenter for Theoretical Biological Physics, Rice University, Houston, TX, USA.ORCID http://orcid.org/0000-0002-1038-0698
Benjamin R DoughtyDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-0447-4468
Kalina AndreevaDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Jacob C UlirschBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-7947-0827
Kaili FanProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0002-8723-7902
Elizabeth M PerezBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Tri C NguyenDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
David R KelleyCalico Life Sciences LLC, South San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-7782-3548
Hilary K FinucaneDepartment of Medicine, Massachusetts General Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0003-3864-9828
Jill E MooreProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0002-3023-0806
Zhiping WengProgram in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.ORCID http://orcid.org/0000-0002-3032-7966
Manolis KellisBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-7113-9630
Michael C BassikDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-5185-8427
Berk UstunHalıcıoğlu Data Science Institute, University of California San Diego, San Diego, CA, USA.
Alkes L PriceDepartment of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.ORCID http://orcid.org/0000-0002-2971-7975
Michael A BeerDepartment of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-9955-3809
Roderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.ORCID http://orcid.org/0000-0002-5738-4477
John A StamatoyannopoulosAltius Institute for Biomedical Sciences, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-2664-5769
Erez Lieberman AidenDepartment of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.ORCID http://orcid.org/0000-0003-0634-6486
William J GreenleafDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1409-3095
Christina S LeslieMemorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-4571-5910
Lars M SteinmetzDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-3962-2865
Anshul KundajeDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-3084-2287
Jesse M EngreitzDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA. engreitz@stanford.edu.ORCID http://orcid.org/0000-0002-5754-1719
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4MINSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2MA Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0MA Data Coordinating Center for ENCODEU41HG006992 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2012 to 2016
$16.6MENCODE Mapping Center-A Comprehensive Catalog of DNase I Hypersensitive SitesUM1HG009444 · NHGRI · ALTIUS INSTITUTE FOR BIOMEDICAL SCIENCES · PI STAMATOYANNOPOULOS, JOHN A · 2017 to 2021
$15.9MStanford Center for Connecting DNA Variants to Function and PhenotypeUM1HG011972 · NHGRI · STANFORD UNIVERSITY · PI JESSE M ENGREITZ, THOMAS QUERTERMOUS · 2021 to 2026
$10.5MEDAC: ENCODE Data Analysis CenterU24HG009446 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GERSTEIN, MARK BENDER, WENG, ZHIPING · 2017 to 2022
$10.4MDeciphering the Genomics of Gene Network Regulation of T Cell and Fibroblast States in Autoimmune InflammationU01HG012103 · NHGRI · SLOAN-KETTERING INST CAN RESEARCH · PI Christina S Leslie, Alexander Y Rudensky · 2021 to 2026
$7.5MHigh-throughput systematic characterization of regulatory element functionUM1HG009436 · NHGRI · STANFORD UNIVERSITY · PI BASSIK, MICHAEL C, GREENLEAF, WILLIAM JAMES · 2017 to 2021
$5.4MPredicting the impact of genetic variants, genes and pathways on human DiseaseU01HG012009 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI ALKES L PRICE, Soumya Raychaudhuri · 2021 to 2026
$4.2MPredicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory codeU01HG012069 · NHGRI · STANFORD UNIVERSITY · PI Anshul Kundaje · 2021 to 2026
$3.9MEncoding genomic architecture in the encyclopedia: linking DNA elements, chromatin state, and gene expression in 3DU01HG009395 · NHGRI · SLOAN-KETTERING INST CAN RESEARCH · PI LESLIE, CHRISTINA S · 2017 to 2021
$3.7MNCI NIH HHS P30 CA008748NHGRI NIH HHS K99 HG009917NHGRI NIH HHS R00 HG009917NHGRI NIH HHS R00 HG012203NHGRI NIH HHS R01 HG011664NHGRI NIH HHS R01 HG012367NHGRI NIH HHS R35 HG011324NHGRI NIH HHS T32 HG000044NHGRI NIH HHS U01 HG009380NHGRI NIH HHS U01 HG009395NHGRI NIH HHS U01 HG009431NHGRI NIH HHS U01 HG012009NHGRI NIH HHS U01 HG012069NHGRI NIH HHS U01 HG012103NHGRI NIH HHS U24 HG009397NHGRI NIH HHS U24 HG009446NHGRI NIH HHS U41 HG006992NHGRI NIH HHS UM1 HG009436NHGRI NIH HHS UM1 HG009444NHGRI NIH HHS UM1 HG011972
Abstract
Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the effect of human genetic variation on disease
Indexed as
Enhancer Elements, GeneticEpistasis, GeneticGene Expression RegulationGene Regulatory NetworksGenome, HumanBenchmarkingBiocurationChromatinGenome-Wide Association StudyHumansPredictive Learning ModelsQuantitative Trait LociChromatin
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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.