ArticleScience (New York, N.Y.)2020
Cell type-specific genetic regulation of gene expression across human tissues.
Abstract read
In one paragraph
Article in Science (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 246 papers, 3 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
246citing papers in PubMed, 3 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
246 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data.Genome biology · 2023Pooled it
- A resource for integrated genomic analysis of the human liver.Scientific reports · 2022Pooled it
- Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits.Nature genetics · 2022Pooled it
- Article
- Prioritizing context-specific genetic risk mechanisms in 11 solid cancers.Journal of the National Cancer Institute · 2026Article
- Single-nucleus atlas of cell-type specific genetic regulation in the human brain.Nature genetics · 2026Article
- Scalable context-dependent single-cell eQTL mapping reveals disease-relevant regulatory variation beyond static models.medRxiv : the preprint server for health sciences · 2026Article
- Catecholamine-mediated release of miR-133a-3p from adipocytes regulates the onset of chronic primary pain.The Journal of clinical investigation · 2026Article
- Post-genome-wide association study variant-to-function challenges in asthma research.The Journal of allergy and clinical immunology · 2026Review
- Where risk resides.Nature immunology · 2026Article
- Mapping genetic regulation of gene expression to cellular contexts identifies long non-coding RNAs associated with brain disorders.Nature communications · 2026Article
- DetectGxT: detecting gene-by-treatment interactions on molecular count phenotypes accounting for allelic additivity.bioRxiv : the preprint server for biology · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Integrating bulk and single-cell RNA sequencing with GWAS reveals regulatory networks underpinning complex traits in beef cattle.Journal of animal science and biotechnology · 2026Article
- Translating genome-wide association studies at multiple scales: Drug target prioritization, cellular architectures, and organ imaging.Cell genomics · 2026Review
- Decoding common and rare noncoding variant effects across cellular and developmental contexts.Nature genetics · 2026Article
- Transcriptome analysis in osteoarthritis primary tissues identifies high-confidence effector genes.Nature communications · 2026Article
- A scalable framework for single-cell eQTL mapping uncovers genetic regulators of meat production traits in pigs.Journal of animal science and biotechnology · 2026Article
- Advances and clinical potential of epigenome editing.Cellular and molecular life sciences : CMLS · 2026Review
- Fine mapping of PTSD GWAS reveals a role for amygdalabioRxiv : the preprint server for biology · 2026Article
186 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
34 authors.
Sarah Kim-Hellmuth *Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany. skimhellmuth@gmail.com tlappalainen@nygenome.org.ORCID http://orcid.org/0000-0001-8791-5729
François Aguet *The Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9414-300X
Meritxell OlivaSection of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-5068-213X
Manuel Muñoz-AguirreCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.ORCID http://orcid.org/0000-0002-6106-7351
Silva KaselaNew York Genome Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-4362-0034
Valentin WucherCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.ORCID http://orcid.org/0000-0002-1331-4549
Stephane E CastelNew York Genome Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-0707-2133
Andrew R HamelThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6420-9573
Ana ViñuelaDepartment of Twin Research and Genetic Epidemiology, King's College London, London, UK.ORCID http://orcid.org/0000-0003-3771-8537
Amy L RobertsDepartment of Twin Research and Genetic Epidemiology, King's College London, London, UK.ORCID http://orcid.org/0000-0002-5704-9249
Serghei MangulDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-4770-3443
Xiaoquan WenDepartment of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
Gao WangDepartment of Human Genetics, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-9336-402X
Alvaro N BarbeiraSection of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-9153-6120
Diego Garrido-MartínCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.ORCID http://orcid.org/0000-0002-4131-4458
Brian B NadelDepartment of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-9583-8169
Yuxin ZouDepartment of Statistics, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-9816-5847
Rodrigo BonazzolaSection of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-8811-2581
Jie QuanInflammation & Immunology, Pfizer, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-7445-0168
Andrew BrownDepartment of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.ORCID http://orcid.org/0000-0002-8087-3033
Angel Martinez-PerezUnit of Genomic of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain.ORCID http://orcid.org/0000-0002-5934-1454
José Manuel SoriaUnit of Genomic of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain.
GTEx Consortium
Gad GetzThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-0936-0753
Emmanouil T DermitzakisDepartment of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.ORCID http://orcid.org/0000-0002-9302-6490
Kerrin S SmallDepartment of Twin Research and Genetic Epidemiology, King's College London, London, UK.ORCID http://orcid.org/0000-0003-4566-0005
Matthew StephensDepartment of Human Genetics, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-5397-9257
Hualin S XiFoundational Neuroscience Center, AbbVie, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-9145-4897
Hae Kyung ImSection of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0003-0333-5685
Roderic GuigóCentre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.ORCID http://orcid.org/0000-0002-5738-4477
Ayellet V SegrèThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6806-5845
Barbara E StrangerSection of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0001-9021-7331
Kristin G ArdlieThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-4272-6283
Tuuli LappalainenNew York Genome Center, New York, NY, USA. skimhellmuth@gmail.com tlappalainen@nygenome.org.ORCID http://orcid.org/0000-0002-7746-8109
Funding
Clinical and Translational Science AwardUL1TR001873 · NCATS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI REILLY, MUREDACH P · 2016 to 2025
$99.0MNew York Center for Collaborative Research In Common Disease Genomics: Genome Aggregation and Joint Variant Calling for CCDG Freeze2UM1HG008901 · NHGRI · NEW YORK GENOME CENTER · PI MANIATIS, THOMAS P, WIGLER, MICHAEL H · 2016 to 2020
$56.6MThe UCSC Genome BrowserU41HG002371 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI KENT, WILLIAM JAMES · 2012 to 2021
$36.6MINSTITUTIONAL TRAINING GRANT IN GENOME SCIENCET32HG000044 · NHGRI · STANFORD UNIVERSITY · PI MICHAEL P. SNYDER · 1995 to 2026
$32.2MScripps Translational Science InstituteUL1TR002550 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI TOPOL, ERIC JEFFREY · 2018 to 2022
$28.9MPilot and Feasibility ProgramP30DK020595 · NIDDK · UNIVERSITY OF CHICAGO · PI Matthew J Brady · 2013 to 2026
$20.9MGenome analysis: statistical methods and applicationsR01HG002585 · NHGRI · UNIVERSITY OF WASHINGTON · PI MATTHEW STEPHENS · 2002 to 2026
$8.4MStructurally complex genome loci in human populations and human phenotypesR01HG006855 · NHGRI · HARVARD MEDICAL SCHOOL · PI Steven Andrew McCarroll · 2012 to 2026
$8.2MA portal and integrative collaborative analysis platform for GTExU41HG009494 · NHGRI · BROAD INSTITUTE, INC. · PI ARDLIE, KRISTIN, GETZ, GAD A · 2017 to 2021
$5.2MStatistical models for fine-mapping and interpretation of schizophrenia-associated lociR01MH106842 · NIMH · NEW YORK GENOME CENTER · PI BUSSEMAKER, HARMEN J, LAPPALAINEN, TUULI · 2015 to 2024
$5.0MStrategic mapping of tissue and population methylation for mental health researchU01MH104393 · NIMH · JOHNS HOPKINS UNIVERSITY · PI FEINBERG, ANDREW P. · 2014 to 2016
$3.9MLIMBIC &MEDULLARY MECH. IN COCAINE-RELATED SUDDEN DEATHR01DA006227 · NIDA · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI MASH, DEBORAH C. · 1990 to 2012
$3.7MCCR NIH HHS HHSN261200800001CMedical Research Council MR/M004422/1Medical Research Council MR/R023131/1NCATS NIH HHS UL1 TR001873NCATS NIH HHS UL1 TR002550NCI NIH HHS HHSN261200800001ENCI NIH HHS R01 CA229618NHGRI NIH HHS F32 HG009987NHGRI NIH HHS K99 HG009916NHGRI NIH HHS R01 HG002585NHGRI NIH HHS R01 HG006855NHGRI NIH HHS R01 HG008150NHGRI NIH HHS R01 HG010067NHGRI NIH HHS R01 HG010480NHGRI NIH HHS R35 HG010718NHGRI NIH HHS T32 HG000044NHGRI NIH HHS U01 HG007593NHGRI NIH HHS U01 HG007598NHGRI NIH HHS U41 HG002371NHGRI NIH HHS U41 HG009494NHGRI NIH HHS UM1 HG008901NHLBI NIH HHS HHSN268201000029CNHLBI NIH HHS R01 HL142028NIDA NIH HHS R01 DA006227NIDDK NIH HHS P30 DK020595NIGMS NIH HHS R01 GM122924NIGMS NIH HHS R01 GM124486NIMH NIH HHS R01 MH090936NIMH NIH HHS R01 MH090937NIMH NIH HHS R01 MH090941NIMH NIH HHS R01 MH090951NIMH NIH HHS R01 MH101814NIMH NIH HHS R01 MH101822NIMH NIH HHS R01 MH106842NIMH NIH HHS R01 MH107666NIMH NIH HHS R01 MH109905NIMH NIH HHS U01 MH104393NLM NIH HHS T32 LM012424Wellcome Trust
Abstract
The Genotype-Tissue Expression (GTEx) project has identified expression and splicing quantitative trait loci in cis (QTLs) for the majority of genes across a wide range of human tissues. However, the functional characterization of these QTLs has been limited by the heterogeneous cellular composition of GTEx tissue samples. We mapped interactions between computational estimates of cell type abundance and genotype to identify cell type-interaction QTLs for seven cell types and show that cell type-interaction expression QTLs (eQTLs) provide finer resolution to tissue specificity than bulk tissue cis-eQTLs. Analyses of genetic associations with 87 complex traits show a contribution from cell type-interaction QTLs and enables the discovery of hundreds of previously unidentified colocalized loci that are masked in bulk tissue.
Indexed as
Gene Expression RegulationQuantitative Trait LociTranscriptomeCellsHumansOrgan SpecificityRNA, Long NoncodingRNA, Long Noncoding
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
Read underepoch 390
Registered trials
None linked
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.