ArticleScientific reports2019
Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- A New Family-Based Approach for Detecting Allele-Specific Expression and for Mapping Possible eQTLs.Animals : an open access journal from MDPI · 2025Article
- Leveraging epigenomes and three-dimensional genome organization for interpreting regulatory variation.PLoS computational biology · 2023Article
- Focus on your locus with a massively parallel reporter assay.Journal of neurodevelopmental disorders · 2022Review
- ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.Nucleic acids research · 2022Article
- Harnessing the Full Potential of Multi-Omic Analyses to Advance the Study and Treatment of Chronic Kidney Disease.Frontiers in nephrology · 2022Review
- Differential Allelic Expression among Long Non-Coding RNAs.Non-coding RNA · 2021Review
- GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.Bioinformatics (Oxford, England) · 2021Article
- INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants.Genome biology · 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
- A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites.Molecular genetics & genomic medicine · 2020Article
- Epigenomics and the kidney.Current opinion in nephrology and hypertension · 2020Review
- regSNPs-ASB: A Computational Framework for Identifying Allele-Specific Transcription Factor Binding From ATAC-seq Data.Frontiers in bioengineering and biotechnology · 2020Article
- HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.Bioinformatics (Oxford, England) · 2018Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several Genome Wide Association Studies (GWAS) have reported variants associated to immune diseases. However, the identified variants are rarely the drivers of the associations and the molecular mechanisms behind the genetic contributions remain poorly understood. ChIP-seq data for TFs and histone modifications provide snapshots of protein-DNA interactions allowing the identification of heterozygous SNPs showing significant allele specific signals (AS-SNPs). AS-SNPs can change a TF binding site resulting in altered gene regulation and are primary candidates to explain associations observed in GWAS and expression studies. We identified 17,293 unique AS-SNPs across 7 lymphoblastoid cell lines. In this set of cell lines we interrogated 85% of common genetic variants in the population for potential regulatory effect and we identified 237 AS-SNPs associated to immune GWAS traits and 714 to gene expression in B cells. To elucidate possible regulatory mechanisms we integrated long-range 3D interactions data to identify putative target genes and motif predictions to identify TFs whose binding may be affected by AS-SNPs yielding a collection of 173 AS-SNPs associated to gene expression and 60 to B cell related traits. We present a systems strategy to find functional gene regulatory variants, the TFs that bind differentially between alleles and novel strategies to detect the regulated genes.
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