ArticlePloS one2014
Allele-specific methylation occurs at genetic variants associated with complex disease.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 43 citations in OpenAlex.
- Meta-evolutionary exome analysis identifies novel type 2 diabetes mellitus genes in the UK Biobank and all of us.PLoS genetics · 2025Pooled it
- A Functional Variant ofJournal of asthma and allergy · 2026Article
- Maternal histone methyltransferases antagonistically regulate autosomal random monoallelic expression (aRMAE) in C. elegans.Nature communications · 2025Article
- Celiac disease: From genetics to epigenetics.World journal of gastroenterology · 2022Review
- cGAS-STING pathway in cancer biotherapy.Molecular cancer · 2020Review
- Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs.Genome biology · 2020Article
- IL-7/IL-7R gene variants impact circulating IL-7/IL-7R homeostasis and ART-associated immune recovery status.Scientific reports · 2019Article
- The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region.Scientific reports · 2019Article
- Global DNA demethylation as an epigenetic marker of human brain metastases.Bioscience reports · 2018Article
- Allele-specific methylation contributed by CpG-SNP is associated with regulation of ALOX5AP gene expression in ischemic stroke.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2018Article
- Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.Science (New York, N.Y.) · 2018Article
- Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease.PloS one · 2018Article
- Cross-generational effects of alcohol dependence in humans on HRAS and TP53 methylation in offspring.Epigenomics · 2017Article
- Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era.Genome biology · 2017Review
- Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.Genome biology · 2017Article
- Constitutional Epi/Genetic Conditions: Genetic, Epigenetic, and Environmental Factors.Journal of pediatric genetics · 2017Review
- Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation.American journal of human genetics · 2016Article
- Tissue-specific patterns of allelically-skewed DNA methylation.Epigenetics · 2016Article
- Article
- In-silico analysis of inflammatory bowel disease (IBD) GWAS loci to novel connections.PloS one · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 7 institutions in 1 country.
Funding
Abstract
We hypothesize that the phenomenon of allele-specific methylation (ASM) may underlie the phenotypic effects of multiple variants identified by Genome-Wide Association studies (GWAS). We evaluate ASM in a human population and document its genome-wide patterns in an initial screen at up to 380,678 sites within the genome, or up to 5% of the total genomic CpGs. We show that while substantial inter-individual variation exists, 5% of assessed sites show evidence of ASM in at least six samples; the majority of these events (81%) are under genetic influence. Many of these cis-regulated ASM variants are also eQTLs in peripheral blood mononuclear cells and monocytes and/or in high linkage-disequilibrium with variants linked to complex disease. Finally, focusing on autoimmune phenotypes, we extend this initial screen to confirm the association of cis-regulated ASM with multiple complex disease-associated variants in an independent population using next-generation bisulfite sequencing. These four variants are implicated in complex phenotypes such as ulcerative colitis and AIDS progression disease (rs10491434), Celiac disease (rs2762051), Crohn's disease, IgA nephropathy and early-onset inflammatory bowel disease (rs713875) and height (rs6569648). Our results suggest cis-regulated ASM may provide a mechanistic link between the non-coding genetic changes and phenotypic variation observed in these diseases and further suggests a route to integrating DNA methylation status with GWAS results.
Indexed as
Identifiers
What OpenQuestion holds
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.