ArticleGenome biology2015
High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 3 of them syntheses that pooled it.
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Who cites it
89 citing papers in PubMed, 3 syntheses or guidelines pooled it, 148 citations in OpenAlex.
- A methylation study implicates the rewiring of brain neural circuits during puberty in the emergence of sex differences in depression symptoms.Journal of child psychology and psychiatry, and allied disciplines · 2022Pooled it
- Epigenetic changes in healthy human skeletal muscle following exercise- a systematic review.Epigenetics · 2019Pooled it
- Epigenetics in eating disorders: a systematic review.Molecular psychiatry · 2019Pooled it
- Article
- Population epigenetics: deciphering DNA methylation diversity and its implications for health, disease, and evolution.Molecular biology and evolution · 2026Review
- An atlas of genetic effects on the monocyte methylome across European and African populations.Genome medicine · 2026Article
- UBD: incorporating uncertainty in cell type proportion estimates from bulk samples to infer cell-type-specific profiles.Briefings in bioinformatics · 2026Article
- Repeated Clozapine Administration Causes Extensive Changes to the Expression of Coding and Non-coding RNAs, Including miR-124, in the Mouse Frontal Cortex.Molecular neurobiology · 2025Article
- A nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon.BMC genomics · 2025Article
- Genetic Architecture of Immune Cell DNA Methylation in the Rhesus Macaque.Molecular ecology · 2025Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.Genome biology · 2025Article
- Epigenetic insights into neuropsychiatric and cognitive symptoms in Parkinson's disease: A DNA co-methylation network analysis.NPJ Parkinson's disease · 2025Article
- Epigenetic variation in light of population genetic practice.Nature communications · 2025Review
- Genome-wide analysis of hepatic DNA methylation reveals impact of epigenetic aging on xenobiotic metabolism and transport genes in an aged mouse model.GeroScience · 2024Article
- Integrative analysis of genetics, epigenetics and RNA expression data reveal three susceptibility loci for smoking behavior in Chinese Han population.Molecular psychiatry · 2024Article
- HBI: a hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data.Genome biology · 2024Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.bioRxiv : the preprint server for biology · 2024Article
- Semimethylation is a feature of diffuse large B-cell lymphoma, and subgroups with poor prognosis are characterized by global hypomethylation and short telomere length.Clinical epigenetics · 2024Article
- Analysis of blood methylation quantitative trait loci in East Asians reveals ancestry-specific impacts on complex traits.Nature genetics · 2024Article
- Investigating the potential of single-cell DNA methylation data to detect allele-specific methylation and imprinting.American journal of human genetics · 2024Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundGenetic influence on DNA methylation is potentially an important mechanism affecting individual differences in humans. We use next-generation sequencing to assay blood DNA methylation at approximately 4.5 million loci, each comprising 2.9 CpGs on average, in 697 normal subjects. Methylation measures at each locus are tested for association with approximately 4.5 million single nucleotide polymorphisms (SNPs) to exhaustively screen for methylation quantitative trait loci (meQTLs).
resultsUsing stringent false discovery rate control, 15 % of methylation sites show genetic influence. Most meQTLs are local, where the associated SNP and methylation site are in close genomic proximity. Distant meQTLs and those spanning different chromosomes are less common. Most local meQTLs encompass common SNPs that alter CpG sites (CpG-SNPs). Local meQTLs encompassing CpG-SNPs are enriched in regions of inactive chromatin in blood cells. In contrast, local meQTLs lacking CpG-SNPs are enriched in regions of active chromatin and transcription factor binding sites. Of 393 local meQTLs that overlap disease-associated regions from genome-wide studies, a high percentage encompass common CpG-SNPs. These meQTLs overlap active enhancers, differentiating them from CpG-SNP meQTLs in inactive chromatin.
conclusionsGenetic influence on the human blood methylome is common, involves several heterogeneous processes and is predominantly dependent on local sequence context at the meQTL site. Most meQTLs involve CpG-SNPs, while sequence-dependent effects on chromatin binding are also important in regions of active chromatin. An abundance of local meQTLs resulting from methylation of CpG-SNPs in inactive chromatin suggests that many meQTLs lack functional consequence. Integrating meQTL and Roadmap Epigenomics data could assist fine-mapping efforts.
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Registered trials
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.