ArticleGenome biology2011
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 522 papers, 3 of them syntheses that pooled it.
What it found
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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.
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Who cites it
522 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- An epigenome-wide association study of early-onset major depression in monozygotic twins.Translational psychiatry · 2020Pooled it
- Elevated DNA methylation across a 48-kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2018Pooled it
- Pooled it
- Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms.Nature communications · 2018Trial
- Epigenetic insights into extreme longevity in the world's oldest terrestrial animal, Jonathan.Science advances · 2026Article
- DNA methylation variability provides a complementary epigenetic signature of aging heterogeneity: Findings from the Canadian Longitudinal Study on Aging and the Baltimore Longitudinal Study of Aging.bioRxiv : the preprint server for biology · 2026Article
- Genetic-epigenetic interactions (meQTLs) in orofacial clefts etiology.Molecular genetics and genomics : MGG · 2026Article
- Dissecting epigenetic heterogeneity in single-cell DNA methylomes with a unified framework.Nature communications · 2026Article
- Early-Life DNA methylation at TRIM6 and TTC23 promoters associates with respiratory infections at one year.Pediatric research · 2026Article
- DNA methylation in the placenta and household socioeconomic status: the SPAH study.Clinical epigenetics · 2026Article
- Integrative epigenomic landscape of Alzheimer's Disease brains reveals oligodendrocyte molecular perturbations associated with tau.Nature communications · 2026Article
- KDM5C and KDM5D influence DNA methylation in adult mouse liver.Biology of sex differences · 2026Article
- Nutriepigenetics and nutriepigenomics: Exploring the interactions between nutrition, epigenetics, and epigenomics in the pathogenesis of noncommunicable diseases.Genetics and molecular biology · 2026Article
- Stress-induced epigenome changes as a risk factor in the onset of mental disorders.Frontiers in psychiatry · 2026Review
- Mendelian randomization analysis of CpG methylation and immune phenotypes in epithelial ovarian cancer outcomes.Epigenetics · 2025Article
- Pharmacoepigenomics in Personalized Medicine: A Hypothesis-Generating Approach to Introduce CpG-PGx SNPs as New Candidates for a Systematic Insight into Genomic-Epigenomic-Phenomic-Pharmacogenomics (G-E-Ph-PGx) Axis.Journal of personalized medicine · 2025Article
- An epigenome-wide analysis of DNA methylation, racialized and economic inequities, and air pollution.Clinical epigenetics · 2025Article
- Genetic-epigenetic interactions (meQTLs) in orofacial clefts etiology.medRxiv : the preprint server for health sciences · 2025Article
- LBX1, ESR1, and ESR2 genes DNA methylation level in idiopathic scoliosis.Scientific reports · 2025Article
- DNA methylation in adaptation to high-altitude environments and pathogenesis of related diseases.Human genomics · 2025Review
462 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
Abstract
backgroundDNA methylation is an essential epigenetic mechanism involved in gene regulation and disease, but little is known about the mechanisms underlying inter-individual variation in methylation profiles. Here we measured methylation levels at 22,290 CpG dinucleotides in lymphoblastoid cell lines from 77 HapMap Yoruba individuals, for which genome-wide gene expression and genotype data were also available.
resultsAssociation analyses of methylation levels with more than three million common single nucleotide polymorphisms (SNPs) identified 180 CpG-sites in 173 genes that were associated with nearby SNPs (putatively in cis, usually within 5 kb) at a false discovery rate of 10%. The most intriguing trans signal was obtained for SNP rs10876043 in the disco-interacting protein 2 homolog B gene (DIP2B, previously postulated to play a role in DNA methylation), that had a genome-wide significant association with the first principal component of patterns of methylation; however, we found only modest signal of trans-acting associations overall. As expected, we found significant negative correlations between promoter methylation and gene expression levels measured by RNA-sequencing across genes. Finally, there was a significant overlap of SNPs that were associated with both methylation and gene expression levels.
conclusionsOur results demonstrate a strong genetic component to inter-individual variation in DNA methylation profiles. Furthermore, there was an enrichment of SNPs that affect both methylation and gene expression, providing evidence for shared mechanisms in a fraction of genes.
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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.