ArticleNucleic acids research2009
Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 73 citations in OpenAlex.
- Allele-Specific Regulation of PAXIP1-AS1 by SMC3/CEBPB at rs112651172 in Psychiatric Disorders Drives Synaptic and Behavioral Dysfunctions in Mice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A Single-Nucleotide Polymorphism in the Promoter of PorcineFrontiers in cell and developmental biology · 2022Article
- Landscape of allele-specific transcription factor binding in the human genome.Nature communications · 2021Article
- Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases.Scientific reports · 2019Article
- A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.PLoS computational biology · 2017Article
- Non-coding single nucleotide variants affecting estrogen receptor binding and activity.Genome medicine · 2016Article
- Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.Human genetics · 2016Article
- Comparative Transcriptional Profiling of Primed and Non-primed Rice Seedlings under Submergence Stress.Frontiers in plant science · 2016Article
- Chromatin structure is distinct between coding and non-coding single nucleotide polymorphisms.BMC molecular biology · 2014Article
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- Interactions between the FTO and GNB3 genes contribute to varied clinical phenotypes in hypertension.PloS one · 2013Article
- A genome-wide screen for genetic variants that modify the recruitment of REST to its target genes.PLoS genetics · 2012Article
- Profiling of the BRCA1 transcriptome through microarray and ChIP-chip analysis.Nucleic acids research · 2011Article
- Identifying functional single nucleotide polymorphisms in the human CArGome.Physiological genomics · 2011Article
- PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs.PloS one · 2010Article
- Genome-wide allele-specific analysis: insights into regulatory variation.Nature reviews. Genetics · 2010Review
- Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.Genome biology · 2009Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledDisease-associated SNPs detected in large-scale association studies are frequently located in non-coding genomic regions, suggesting that they may be involved in transcriptional regulation. Here we describe a new strategy for detecting regulatory SNPs (rSNPs), by combining computational and experimental approaches. Whole genome ChIP-chip data for USF1 was analyzed using a novel motif finding algorithm called BCRANK. 1754 binding sites were identified and 140 candidate rSNPs were found in the predicted sites. For validating their regulatory function, seven SNPs found to be heterozygous in at least one of four human cell samples were investigated by ChIP and sequence analysis (haploChIP). In four of five cases where the SNP was predicted to affect binding, USF1 was preferentially bound to the allele containing the consensus motif. Allelic differences in binding for other proteins and histone marks further reinforced the SNPs regulatory potential. Moreover, for one of these SNPs, H3K36me3 and POLR2A levels at neighboring heterozygous SNPs indicated effects on transcription. Our strategy, which is entirely based on in vivo data for both the prediction and validation steps, can identify individual binding sites at base pair resolution and predict rSNPs. Overall, this approach can help to pinpoint the causative SNPs in complex disorders where the associated haplotypes are located in regulatory regions. AVAILABILITY: BCRANK is available from Bioconductor (http://www.bioconductor.org/).
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