ArticleNature communications2024
Whole-genome sequencing in 333,100 individuals reveals rare non-coding single variant and aggregate associations with height.
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Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
- Evolution-guided yeast complementation reveals functional differences in human PSPH variants.FEBS open bio · 2026Article
- Whole-genome sequencing implicates rare, low-frequency and structural non-coding variation at themedRxiv : the preprint server for health sciences · 2026Article
- Decoding common and rare noncoding variant effects across cellular and developmental contexts.Nature genetics · 2026Article
- Advances and challenges of splicing prediction with AI.Nature genetics · 2026Review
- Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs.Communications biology · 2026Article
- An empirical Bayes framework for burden and dispersion association tests helps prioritize rare variants associated with Alzheimer's disease.medRxiv : the preprint server for health sciences · 2026Article
- Analysis of whole genome sequencing and plasma metabolomics unveil genetic determinants and clinical implications for human health.Nature communications · 2026Article
- Integrating common and rare variants improves polygenic risk prediction across diverse populations.Nature communications · 2026Article
- Application of the STAAR framework in detecting rare variant associations with Alzheimer disease and related dementias: Insights and implications.HGG advances · 2026Article
- Rare coding and noncoding variants map 1,342 diseases and biomarkers in 490,549 whole genomes.medRxiv : the preprint server for health sciences · 2026Article
- Scalable and accurate rare-variant association tests for whole genome sequencing time-to-event analysis in large biobanks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Impact of control selection strategies on GWAS results: a study of prostate cancer in the UK Biobank.Briefings in bioinformatics · 2026Article
- Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations.Nature communications · 2026Article
- Archipelago Method for Variant Set Association Test Statistics.Genetic epidemiology · 2026Article
- Functional analysis of NPR2 variants supports the therapeutic rationale for CNP in short stature.American journal of human genetics · 2026Article
- Article
- Individuals whose phenotype deviates from genetic expectation defined by common variation are enriched for rare damaging variants in genes that cause rare disease.medRxiv : the preprint server for health sciences · 2025Article
- Streamlining large-scale genomic data management: Insights from the UK Biobank whole-genome sequencing data.Cell genomics · 2025Article
- Genomics of schizophrenia, bipolar disorder and major depressive disorder.Nature reviews. Genetics · 2025Review
- Whole-genome sequencing reveals rare and structural variants contributing to psoriasis and identifies CERCAM as a risk gene.Cell genomics · 2025Article
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Authors and funding
58 authors.
Gareth Hawkes *Clinical and Biomedical Sciences, University of Exeter, Exeter, UK. g.hawkes2@exeter.ac.uk.ORCID 0000-0002-3367-789X
Robin N Beaumont *Clinical and Biomedical Sciences, University of Exeter, Exeter, UK.ORCID 0000-0003-0750-8248
Zilin Li *Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Ravi Mandla *Department of Medicine, Harvard Medical School, Broad Institute, Boston, Massachusetts, USA.
Xihao Li *Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID 0000-0001-8151-0106
Christine M AlbertDepartment of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.ORCID 0000-0002-2081-1121
Donna K ArnettProvost Office, University of South Carolina, Columbia, SC, USA.
Allison E Ashley-KochDepartment of Medicine, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA.ORCID 0000-0001-5409-9155
Aneel A AshraniDivision of Hematology, Department of Medicine, Mayo Clinic Rochester, Rochester, MN, USA.
Kathleen C BarnesDepartment of Medicine, School of Medicine, University of Colorado, Aurora, CO, USA.ORCID 0000-0002-3030-4705
Eric BoerwinkleHuman Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
Jennifer A BrodyCardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.ORCID 0000-0001-8509-148X
April P CarsonDepartment of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.ORCID 0000-0002-7970-6756
Nathalie ChamiThe Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID 0000-0002-8547-6424
Yii-Der Ida ChenThe Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA.
Mina K ChungDepartment of Cardiovascular Medicine, Heart, Vascular & Thoracic Institute, Cleveland, OH, USA.
Joanne E CurranDepartment of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA.ORCID 0000-0002-6898-155X
Dawood DarbarDivision of Cardiology, Department of Medicine, University of Illinois Chicago, Chicago, IL, USA.ORCID 0000-0002-4103-5977
Patrick T EllinorCardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.ORCID 0000-0002-2067-0533
Myrian FornageHuman Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.ORCID 0000-0003-0677-8158
Victor R GordeukDepartment of Medicine, School of Medicine, University of Illinois at Chicago, Chicago, IL, USA.ORCID 0000-0003-4725-7295
Xiuqing GuoThe Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA.ORCID 0000-0002-5264-5068
Jiang HeDepartment of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.
Chii-Min HwuSection of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei City, Taiwan.
Rita R KalyaniGeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Robert KaplanDepartment of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
Sharon L R KardiaDepartment of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
Charles KooperbergDivision of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-7986-8560
Ruth J F LoosThe Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID 0000-0002-8532-5087
Steven A LubitzCardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.ORCID 0000-0002-9599-4866
Ryan L MinsterDepartment of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.ORCID 0000-0001-7382-6717
Take NaseriNaseri & Associates Public Health Consultancy Firm and Family Health Clinic, Apia, Samoa.
Satupa'itea VialiOceania University of Medicine, Apia, Samoa.
Braxton D MitchellDepartment of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID 0000-0003-4920-4744
Joanne M MurabitoBoston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA.
Nicholette D PalmerDepartment of Biochemistry, Wake Forest University School of Medicine, Winston-, Salem, NC, USA.ORCID 0000-0001-8883-2511
Bruce M PsatyCardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA.ORCID 0000-0002-7278-2190
Susan RedlineDivision of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA.
M Benjamin ShoemakerDepartment of Medicine, Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
Edwin K SilvermanChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Marilyn J TelenDepartment of Medicine, Duke University School of Medicine, Durham, NC, USA.ORCID 0000-0003-3809-1780
Scott T WeissChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.ORCID 0000-0001-7196-303X
Lisa R YanekGeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.ORCID 0000-0001-7117-1075
Hufeng ZhouDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.ORCID 0000-0001-9382-5674
NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
Ching-Ti LiuDepartment of Biostatistics, School of Public Health, Boston University, Boston, MA, USA.ORCID 0000-0002-0703-0742
Kari E NorthDepartment of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID 0000-0002-8903-0366
Anne E JusticePopulation Health Sciences, Geisinger, Danville, PA, USA.ORCID 0000-0002-8903-8712
Jonathan M LockeClinical and Biomedical Sciences, University of Exeter, Exeter, UK.
Nick OwensClinical and Biomedical Sciences, University of Exeter, Exeter, UK.ORCID 0000-0002-2151-9923
Anna MurrayClinical and Biomedical Sciences, University of Exeter, Exeter, UK.ORCID 0000-0002-2351-2522
Kashyap PatelClinical and Biomedical Sciences, University of Exeter, Exeter, UK.ORCID 0000-0002-9240-8104
Timothy M FraylingClinical and Biomedical Sciences, University of Exeter, Exeter, UK.ORCID 0000-0001-8362-2603
Caroline F WrightClinical and Biomedical Sciences, University of Exeter, Exeter, UK.ORCID 0000-0003-2958-5076
Andrew R WoodClinical and Biomedical Sciences, University of Exeter, Exeter, UK.ORCID 0000-0003-1726-948X
Xihong LinDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.ORCID 0000-0001-7067-7752
Alisa ManningDepartment of Medicine, Harvard Medical School, Broad Institute, Boston, Massachusetts, USA.ORCID 0000-0003-0247-902X
Michael N WeedonClinical and Biomedical Sciences, University of Exeter, Exeter, UK. m.n.weedon@exeter.ac.uk.ORCID 0000-0002-6174-6135
Funding
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Hazel B Nichols · 2001 to 2026
$36.3MStatistical Methods for Analysis of Massive Genetic and Genomic Data in Cancer ResearchR35CA197449 · NCI · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI XIHONG LIN · 2015 to 2026
$10.9MCHARGE Consortium: Omics Discovery for CVD and Aging PhenotypesR01HL105756 · NHLBI · UNIVERSITY OF WASHINGTON · PI Bruce M Psaty, NICHOLAS L SMITH · 2011 to 2026
$9.5MStatistical Methods for Integrative Analysis of Large-Scale Whole Genome Sequencing Studies and Biobanks of Common DiseasesR01HL163560 · NHLBI · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI XIHONG LIN · 2022 to 2026
$2.6MInnovative Medicines Initiative (IMI) 875534Medical Research Council MR/M008924/1NCI NIH HHS R35 CA197449NHLBI NIH HHS R01 HL105756NHLBI NIH HHS R01 HL163560NIEHS NIH HHS P30 ES010126Wellcome Trust
Abstract
The role of rare non-coding variation in complex human phenotypes is still largely unknown. To elucidate the impact of rare variants in regulatory elements, we performed a whole-genome sequencing association analysis for height using 333,100 individuals from three datasets: UK Biobank (N = 200,003), TOPMed (N = 87,652) and All of Us (N = 45,445). We performed rare ( < 0.1% minor-allele-frequency) single-variant and aggregate testing of non-coding variants in regulatory regions based on proximal-regulatory, intergenic-regulatory and deep-intronic annotation. We observed 29 independent variants associated with height at P <
Indexed as
Body HeightGenome-Wide Association StudyPolymorphism, Single NucleotideWhole Genome SequencingFemaleGene FrequencyGenetic VariationGenome, HumanHumansMalePhenotype
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