ArticleAmerican journal of human genetics2021
Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression.
Article in American journal of human genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 47 citations in OpenAlex.
- TRAD: a functional annotation resource for human tandem repeats.Science China. Life sciences · 2026Article
- Integrative screening identifies functional variants and VNTRs underlying GWAS signals at the 5p15.33 multi-cancer susceptibility locus.medRxiv : the preprint server for health sciences · 2026Article
- TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data.Genome biology · 2025Article
- A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank.Nature communications · 2024Article
- Modification of Huntington's disease by short tandem repeats.Brain communications · 2024Article
- Rediscovering tandem repeat variation in schizophrenia: challenges and opportunities.Translational psychiatry · 2023Review
- Advances in the discovery and analyses of human tandem repeats.Emerging topics in life sciences · 2023Review
- A novel microdeletion of 517 kb downstream of the PAX6 gene in a Chinese family with congenital aniridia.BMC ophthalmology · 2023Article
- Article
- vamos: variable-number tandem repeats annotation using efficient motif sets.Genome biology · 2023Article
- Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire.Nature communications · 2023Article
- A novel hypervariable variable number tandem repeat in the dopamine transporter gene (Life science alliance · 2023Article
- The motif composition of variable number tandem repeats impacts gene expression.Genome research · 2023Article
- Native functions of short tandem repeats.eLife · 2023Article
- Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation.Genome research · 2023Article
- A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits.American journal of human genetics · 2022Article
- Curated variation benchmarks for challenging medically relevant autosomal genes.Nature biotechnology · 2022Article
- Recent advances and current challenges in population genomics of structural variation in animals and plants.Frontiers in genetics · 2022Review
- Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution.Molecular psychiatry · 2022Review
- Modification mapping by nanopore sequencing.Frontiers in genetics · 2022Review
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Variable number tandem repeats (VNTRs) are composed of large tandemly repeated motifs, many of which are highly polymorphic in copy number. However, because of their large size and repetitive nature, they remain poorly studied. To investigate the regulatory potential of VNTRs, we used read-depth data from Illumina whole-genome sequencing to perform association analysis between copy number of ∼70,000 VNTRs (motif size ≥ 10 bp) with both gene expression (404 samples in 48 tissues) and DNA methylation (235 samples in peripheral blood), identifying thousands of VNTRs that are associated with local gene expression (eVNTRs) and DNA methylation levels (mVNTRs). Using an independent cohort, we validated 73%-80% of signals observed in the two discovery cohorts, while allelic analysis of VNTR length and CpG methylation in 30 Oxford Nanopore genomes gave additional support for mVNTR loci, thus providing robust evidence to support that these represent genuine associations. Further, conditional analysis indicated that many eVNTRs and mVNTRs act as QTLs independently of other local variation. We also observed strong enrichments of eVNTRs and mVNTRs for regulatory features such as enhancers and promoters. Using the Human Genome Diversity Panel, we define sets of VNTRs that show highly divergent copy numbers among human populations and show that these are enriched for regulatory effects and preferentially associate with genes that have been linked with human phenotypes through GWASs. Our study provides strong evidence supporting functional variation at thousands of VNTRs and defines candidate sets of VNTRs, copy number variation of which potentially plays a role in numerous human phenotypes.
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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.