ArticleHuman genetics2016
Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.
Article in Human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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
33 citing papers in PubMed, 62 citations in OpenAlex.
- Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.Bioinformatics (Oxford, England) · 2026Article
- baal-nf identifies motif-disrupting variants that decrease transcription factor binding affinity.Genome biology · 2026Article
- Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis.Nature communications · 2025Article
- Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis.Genome research · 2025Article
- SNPeBoT: a tool for predicting transcription factor allele specific binding.BMC bioinformatics · 2025Article
- Regulatory Plasticity of the Human Genome.Molecular biology and evolution · 2025Article
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Current progress and future perspective of super-enhancers: a viable and effective bridge between the transcriptional apparatus and disease.Frontiers in genetics · 2025Review
- Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data.Genome biology · 2024Article
- A regulatory element associated to NAFLD in the promoter of DIO1 controls LDL-C, HDL-C and triglycerides in hepatic cells.Lipids in health and disease · 2024Article
- Exploring the Genetic Predisposition to Epigenetic Changes in Alzheimer's Disease.International journal of molecular sciences · 2023Article
- Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach.PLoS computational biology · 2022Article
- Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression.Genome research · 2022Article
- Augmenting and directing long-range CRISPR-mediated activation in human cells.Nature methods · 2021Article
- A Panel of rSNPs Demonstrating Allelic Asymmetry in Both ChIP-seq and RNA-seq Data and the Search for Their Phenotypic Outcomes through Analysis of DEGs.International journal of molecular sciences · 2021Article
- Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases.International journal of molecular sciences · 2021Review
- Landscape of allele-specific transcription factor binding in the human genome.Nature communications · 2021Article
- Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data.International journal of molecular sciences · 2020Article
- Disease-associated KIF3A variants alter gene methylation and expression impacting skin barrier and atopic dermatitis risk.Nature communications · 2020Article
- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association studies (GWAS) have identified a large number of disease-associated SNPs, but in few cases the functional variant and the gene it controls have been identified. To systematically identify candidate regulatory variants, we sequenced ENCODE cell lines and used public ChIP-seq data to look for transcription factors binding preferentially to one allele. We found 9962 candidate regulatory SNPs, of which 16 % were rare and showed evidence of larger functional effect than common ones. Functionally rare variants may explain divergent GWAS results between populations and are candidates for a partial explanation of the missing heritability. The majority of allele-specific variants (96 %) were specific to a cell type. Furthermore, by examining GWAS loci we found >400 allele-specific candidate SNPs, 141 of which were highly relevant in our cell types. Functionally validated SNPs support identification of an SNP in SYNGR1 which may expose to the risk of rheumatoid arthritis and primary biliary cirrhosis, as well as an SNP in the last intron of COG6 exposing to the risk of psoriasis. We propose that by repeating the ChIP-seq experiments of 20 selected transcription factors in three to ten people, the most common polymorphisms can be interrogated for allele-specific binding. Our strategy may help to remove the current bottleneck in functional annotation of the genome.
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.