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Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation
Open accessPublished version of a preprint
Abstract
Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.
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“In males, among the 126 CpGs mapped to the AD-associated CpGs or located in AD-associated DMRs (Supplementary Tables 2, 5), 67 CpGs had cis mQTLs, and 3 CpGs had both cis [58] and trans mQTLs.”
From Distinct sex-specific DNA methylation differences in Alzheimer’s disease (2022) · cites this paper as [58]
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“These results are consistent with the previous observation that a substantial proportion (about 45%) of the DNA methylation sites targeted by the Illumina 450k array are influenced by genetic variants in the blood [58].”
From Distinct sex-specific DNA methylation differences in Alzheimer’s disease (2022) · cites this paper as [58]
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“EWAS addressing the joint effect of genotype and environment are still in its infancy (Min et al., 2021).”
From Can epigenetics shine a light on the biological pathways underlying major mental disorders? (2022) · cites this paper as Min et al., 2021
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“the G allele of the lead variant rs911196 increases methylation of cg01799681, cg16867657, cg21572722, and cg23642061 in whole blood (62, 63)”
From Retinal polyunsaturated fatty acid supplementation reverses aging-related vision decline in mice (2025) · cites this paper as [63]
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“We compared our results with the Genetics of DNAm Consortium database of meQTLs 21 and the Chronic Renal Insuf fi - ciency Cohort Human Whole Blood methylation quantitative trait locus Atlas 22 and determined whether variants were annotated as whole-blood expression QTLs (eQTLs) in the…”
Kaczmarczyk, B., de la Calle-Fabregat, C., Conde, A., Duarte, A. C., Mena-Vázquez, N., Fernández-Nebro, A., Triguero-Martinez, A., Castañeda, S., Sobrin, R. D.-S., Mera-Varela, A., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-99755-6
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“62 Among the 56 significant individual CpGs (Supplementary Table 1) and the 134 CpGs located in significant DMRs (Supplementary Table 2), 93 CpGs had 97988 mQTLs in cis and 19 CpGs had 4702 mQTLs in trans in the blood (Supplementary Table 6).”
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BackgroundMethodResultInfluentialGendre, B., Martinez-Perez, A., Kleber, M., Vlieg, A. V. H., Boland, A., Olaso, R., Germain, M., Munsch, G., Moissl, A., Suchon, P., et al. (2024) · bioRxiv · doi:10.1101/2024.02.08.579474
“…(p = 5.9 x 10 -7 ) with whole blood DNA methylation levels at CA13 cg0571334 CpG site in the GoDMC database (http://mqtldb.godmc.org.uk/index) [35], rs75463553 demonstrated strong associations with whole blood DNA methylation at several CpG sites at the PSKH2 locus (Supplementary Figure S3)…”
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Self-citation
Metadata
- Authors
- Min, J. L., Hemani, G., Hannon, E., Dekkers, K. F., Castillo-Fernandez, J., Luijk, R., Carnero-Montoro, E., Lawson, D. J., Burrows, K., Suderman, M., Bretherick, A. D., Richardson, T. G., Klughammer, J., Iotchkova, V., Sharp, G., Al Khleifat, A., Shatunov, A., Iacoangeli, A., McArdle, W. L., Ho, K. M., Kumar, A., Söderhäll, C., Soriano-Tárraga, C., Giralt-Steinhauer, E., Kazmi, N., Mason, D., McRae, A. F., Corcoran, D. L., Sugden, K., Kasela, S., Cardona, A., Day, F. R., Cugliari, G., Viberti, C., Guarrera, S., Lerro, M., Gupta, R., Bollepalli, S., Mandaviya, P., Zeng, Y., Clarke, T.-K., Walker, R. M., Schmoll, V., Czamara, D., Ruiz-Arenas, C., Rezwan, F. I., Marioni, R. E., Lin, T., Awaloff, Y., Germain, M., Aïssi, D., Zwamborn, R., van Eijk, K., Dekker, A., van Dongen, J., Hottenga, J.-J., Willemsen, G., Xu, C.-J., Barturen, G., Català-Moll, F., Kerick, M., Wang, C., Melton, P., Elliott, H. R., Shin, J., Bernard, M., Yet, I., Smart, M., Gorrie-Stone, T., BIOS Consortium, Shaw, C., Al Chalabi, A., Ring, S. M., Pershagen, G., Melén, E., Jiménez-Conde, J., Roquer, J., Lawlor, D. A., Wright, J., Martin, N. G., Montgomery, G. W., Moffitt, T. E., Poulton, R., Esko, T., Milani, L., Metspalu, A., Perry, J. R. B., Ong, K. K., Wareham, N. J., Matullo, G., Sacerdote, C., Panico, S., Caspi, A., Arseneault, L., Gagnon, F., Ollikainen, M., Kaprio, J., Felix, J. F., Rivadeneira, F., Tiemeier, H., van IJzendoorn, M. H., Uitterlinden, A. G., Jaddoe, V. W. V., Haley, C., McIntosh, A. M., Evans, K. L., Murray, A., Räikkönen, K., Lahti, J., Nohr, E. A., Sørensen, T. I. A., Hansen, T., Morgen, C. S., Binder, E. B., Lucae, S., Gonzalez, J. R., Bustamante, M., Sunyer, J., Holloway, J. W., Karmaus, W., Zhang, H., Deary, I. J., Wray, N. R., Starr, J. M., Beekman, M., van Heemst, D., Slagboom, P. E., Morange, P.-E., Trégouët, D.-A., Veldink, J. H., Davies, G. E., de Geus, E. J. C., Boomsma, D. I., Vonk, J. M., Brunekreef, B., Koppelman, G. H., Alarcón-Riquelme, M. E., Huang, R.-C., Pennell, C. E., van Meurs, J., Ikram, M. A., Hughes, A. D., Tillin, T., Chaturvedi, N., Pausova, Z., Paus, T., Spector, T. D., Kumari, M., Schalkwyk, L. C., Visscher, P. M., Davey Smith, G., Bock, C., Gaunt, T. R., Bell, J. T., Heijmans, B. T., Mill, J., & Relton, C. L.
- Affiliations
- University of Bristol (GB)
- University of Exeter (GB)
- Leiden University Medical Center (NL)
- Institute of Genetics and Cancer (GB)
- Austrian Academy of Sciences (AT)
- MRC Weatherall Institute of Molecular Medicine (GB)
- King's College London (GB)
- Swiss Tropical and Public Health Institute (CH)
- Karolinska Institutet (SE)
- Bradford Institute for Health Research (GB)
- The University of Queensland (AU)
- Duke University (US)
- University of Tartu (EE)
- University of Cambridge (GB)
- Italian institute for Genomic Medicine (IT)
- University of Toronto (CA)
- University of Helsinki (FI)
- Erasmus MC (NL)
- Sun Yat-sen University (CN)
- Royal Edinburgh Hospital (GB)
- Western General Hospital (GB)
- Max Planck Institute of Psychiatry (DE)
- Universitat Pompeu Fabra (ES)
- Aberystwyth University (GB)
- Université de Bordeaux (FR)
- Universität Hamburg (DE)
- University Medical Center Utrecht (NL)
- Amsterdam Public Health (NL)
- University Medical Center Groningen (NL)
- Universidad de Granada (ES)
- Consejo Superior de Investigaciones Científicas (ES)
- University of Newcastle Australia (AU)
- University of Tasmania (AU)
- University of Essex (GB)
- King's College Hospital (GB)
- Hospital Del Mar (ES)
- QIMR Berghofer Medical Research Institute (AU)
- University of Otago (NZ)
- Broad Institute (US)
- Federico II University Hospital (IT)
- Harvard University (US)
- University College London (GB)
- University of Aberdeen (GB)
- University of Southern Denmark (DK)
- University of Copenhagen (DK)
- Emory University (US)
- University of Southampton (GB)
- University of Memphis (US)
- University of Edinburgh (GB)
- Alzheimer Scotland (GB)
- Inserm (FR)
- Avera Institute for Human Genetics (US)
- Utrecht University (NL)
- The Kids Research Institute Australia (AU)
- Corresponding author
- Min, Josine L.
- ORCID
- Min, Josine L.
- Hemani, Gibran
- Hannon, Eilis
- Dekkers, Koen F.
- Castillo-Fernandez, Juan
- Lawson, Daniel J.
- Burrows, Kimberley
- Suderman, Matthew
- Bretherick, Andrew D.
- Richardson, Tom G.
- Klughammer, Johanna
- Iotchkova, Valentina
- Sharp, Gemma
- Al Khleifat, Ahmad
- Shatunov, Aleksey
- Iacoangeli, Alfredo
- McArdle, Wendy L.
- Ho, Karen M.
- Kumar, Ashish
- Söderhäll, Cilla
- Soriano-Tárraga, Carolina
- Kazmi, Nabila
- Mason, Dan
- McRae, Allan F.
- Corcoran, David L.
- Sugden, Karen
- Kasela, Silva
- Cardona, Alexia
- Day, Felix R.
- Cugliari, Giovanni
- Guarrera, Simonetta
- Gupta, Richa
- Bollepalli, Sailalitha
- Mandaviya, Pooja
- Zeng, Yanni
- Clarke, Toni-Kim
- Walker, Rosie M.
- Schmoll, Vanessa
- Czamara, Darina
- Ruiz-Arenas, Carlos
- Rezwan, Faisal I.
- Marioni, Riccardo E.
- Lin, Tian
- Germain, Marine
- Aïssi, Dylan
- Zwamborn, Ramona
- van Eijk, Kristel
- van Dongen, Jenny
- Hottenga, Jouke-Jan
- Willemsen, Gonneke
- Xu, Cheng-Jian
- Barturen, Guillermo
- Kerick, Martin
- Wang, Carol
- Melton, Phillip
- Elliott, Hannah R.
- Shin, Jean
- Bernard, Manon
- Yet, Idil
- Smart, Melissa
- Gorrie-Stone, Tyler
- Al Chalabi, Ammar
- Ring, Susan M.
- Pershagen, Göran
- Melén, Erik
- Jiménez-Conde, Jordi
- Roquer, Jaume
- Lawlor, Deborah A.
- Wright, John
- Martin, Nicholas G.
- Montgomery, Grant W.
- Moffitt, Terrie E.
- Poulton, Richie
- Esko, Tõnu
- Milani, Lili
- Metspalu, Andres
- Perry, John R. B.
- Ong, Ken K.
- Wareham, Nicholas J.
- Matullo, Giuseppe
- Sacerdote, Carlotta
- Panico, Salvatore
- Caspi, Avshalom
- Arseneault, Louise
- Ollikainen, Miina
- Kaprio, Jaakko
- Felix, Janine F.
- Rivadeneira, Fernando
- Tiemeier, Henning
- van IJzendoorn, Marinus H.
- Uitterlinden, André G.
- Jaddoe, Vincent W. V.
- Haley, Chris
- McIntosh, Andrew M.
- Evans, Kathryn L.
- Murray, Alison
- Räikkönen, Katri
- Lahti, Jari
- Nohr, Ellen A.
- Sørensen, Thorkild I. A.
- Hansen, Torben
- Morgen, Camilla S.
- Binder, Elisabeth B.
- Lucae, Susanne
- Gonzalez, Juan Ramon
- Bustamante, Mariona
- Sunyer, Jordi
- Holloway, John W.
- Karmaus, Wilfried
- Zhang, Hongmei
- Deary, Ian J.
- Wray, Naomi R.
- Starr, John M.
- Beekman, Marian
- van Heemst, Diana
- Slagboom, P. Eline
- Morange, Pierre-Emmanuel
- Trégouët, David-Alexandre
- Veldink, Jan H.
- de Geus, Eco J. C.
- Boomsma, Dorret I.
- Vonk, Judith M.
- Brunekreef, Bert
- Koppelman, Gerard H.
- Alarcón-Riquelme, Marta E.
- Huang, Rae-Chi
- Pennell, Craig E.
- van Meurs, Joyce
- Ikram, M. Arfan
- Hughes, Alun D.
- Tillin, Therese
- Chaturvedi, Nish
- Pausova, Zdenka
- Paus, Tomas
- Spector, Timothy D.
- Schalkwyk, Leonard C.
- Visscher, Peter M.
- Davey Smith, George
- Bock, Christoph
- Gaunt, Tom R.
- Bell, Jordana T.
- Heijmans, Bastiaan T.
- Mill, Jonathan
- Relton, Caroline L.
- Venue
- Nature Genetics
- Published
- 2021-09
- Volume
- 53
- Issue
- 9
- Pages
- 1311-1321
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC7612069
- OpenAlex
- W3113754461
- Cited by
- 506
- References
- 88
- Citations by year
- 2026: 77 · 2025: 107 · 2024: 117 · 2023: 86 · 2022: 88 · 2021: 29
- FWCI
- 26.69
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Genetics (publishedVersion)
- medRxiv (acceptedVersion, cc-by-nc-nd)
- UWA Profiles and Research Repository (UWA) (publishedVersion, other-oa)
- University of Southern Denmark Research Portal (University of Southern Denmark) (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion, other-oa)
- Bristol Research (University of Bristol) (publishedVersion, other-oa)
- VU Research Portal (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- Open Access at Essex (University of Essex) (acceptedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- UTAS Research Repository (submittedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- HAL (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion, cc-by)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- edoc (University of Basel) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion)
- Työväentutkimus Vuosikirja (submittedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion)
- Research Portal (King's College London) (submittedVersion, other-oa)
- Research Portal (King's College London) (submittedVersion)
- Oskar-Bordeaux (Universite de Bordeaux) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- NOVA (University of Newcastle Australia) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (208806/Z/17/Z, 204979/Z/16/Z)
- Royal Society (208806/Z/17/Z)
- RCUK | Medical Research Council (MR/R005176/1, MR/K013807/1, MR/M008924/1, MC_UU_00011/5, MC_UU_00011/1, MC_UU_00011/4)
- Österreichischen Akademie der Wissenschaften (doc fellowship)
- RCUK | Biotechnology and Biological Sciences Research Council (BB/S020845/1)
- RCUK | Economic and Social Research Council (ES/N000404/1)
- ZonMw (529051021)
- Netherlands CardioVascular Research Initiative
- Cancer Research UK (C18281/A191169)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- DNA methylation, DNA methylation quantitative trait loci, genetic variants, blood DNA methylation, polygenic architecture, trans-eQTL, gene networks, complex diseases, genotype-phenotype correlation, gene expression regulation
- MeSH terms
- Chromosome Mapping, DNA, Gene Expression Regulation, Humans, DNA Methylation, Quantitative Trait, Heritable, Genetic Predisposition to Disease, Multifactorial Inheritance, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Epigenesis, Genetic, Genome-Wide Association Study, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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