ArticleNucleic acids research2016
Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers, 2 of them syntheses that pooled it.
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Who cites it
102 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.Nature protocols · 2026Guideline
- Genome-wide contribution of common short-tandem repeats to Parkinson's disease genetic risk.Brain : a journal of neurology · 2023Pooled it
- TRAD: a functional annotation resource for human tandem repeats.Science China. Life sciences · 2026Article
- Tandem repeats in human brain evolution and disease susceptibility.Molecules and cells · 2026Review
- The contribution of short tandem repeats to splicing variation in the human cortex.bioRxiv : the preprint server for biology · 2026Article
- Defining a tandem repeat catalog and variation clusters for genome-wide analyses.bioRxiv : the preprint server for biology · 2026Article
- Comparative Analysis of the EF-1α Intergenic Region inInternational journal of molecular sciences · 2026Article
- The evolution of tandem repeat sequences under partial selfing and different modes of selection.Heredity · 2026Article
- A Statistical Framework to Infer the Mutation Model of Tandem Repeat Variants.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats.Genome biology and evolution · 2026Review
- The repertoire of short tandem repeats across the tree of life.Genome biology · 2025Article
- Genome-wide selection inference at short tandem repeats.PLoS genetics · 2025Article
- Multi-marker GWAS and variant-specific genomic prediction for growth traits in Pacific white shrimp.Scientific reports · 2025Article
- Emerging drivers of DNA repeat expansions.Biochemical Society transactions · 2025Review
- Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis.Genome biology · 2025Article
- Characterization and comparative analysis of the complete mitochondrial genome of Phlomoides rotata, a traditional Tibetan medicinal plant.BMC genomics · 2025Article
- Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms.Briefings in bioinformatics · 2025Article
- Whole Genome Variable Number Tandem Repeat Analysis in Alzheimer Disease.Neurology. Genetics · 2025Article
- Scalable eQTL mapping using single-nucleus RNA-sequencing of recombined gametes from a small number of individuals.PLoS biology · 2025Article
- Article
42 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation. We identified >100 TRs associated with expression/methylation levels of adjacent genes. These potential eQTL/mQTL TRs were enriched for overlaps with transcription factor binding and DNaseI hypersensitivity sites, providing a rationale for their effects. Moreover, we showed that most TR variants are poorly tagged by nearby single nucleotide polymorphisms (SNPs) markers, indicating that many functional TR variants are not effectively assayed by SNP-based approaches. Our study assigns biological significance to TR variations in the human genome, and suggests that a significant fraction of TR variations exert functional effects via alterations of local gene expression or epigenetics. We conclude that targeted studies that focus on genotyping TR variants are required to fully ascertain functional variation in the genome.
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