ArticleBMC genomics2005
Identification of functional SNPs in the 5-prime flanking sequences of human genes.
Article in BMC genomics, 2005. 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, 62 citations in OpenAlex.
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- The Role of Genetic Polymorphisms in Diabetic Retinopathy: Narrative Review.International journal of molecular sciences · 2023Review
- Genetic mutations in NF-κB pathway genes were associated with the protection from hepatitis C virus infection among Chinese Han population.Scientific reports · 2019Article
- Effects of gene polymorphisms in the endoplasmic reticulum stress pathway on clinical outcomes of chemoradiotherapy in Chinese patients with nasopharyngeal carcinoma.Acta pharmacologica Sinica · 2017Article
- Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.Human mutation · 2016Article
- A novel type 2 diabetes risk allele increases the promoter activity of the muscle-specific small ankyrin 1 gene.Scientific reports · 2016Article
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- Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding.PLoS genetics · 2012Article
- Prediction of functional regulatory SNPs in monogenic and complex disease.Human mutation · 2011Article
- A 5'-region polymorphism modulates promoter activity of the tumor suppressor gene MFSD2A.Molecular cancer · 2011Article
- Novel cleft susceptibility genes in chromosome 6q.Journal of dental research · 2010Article
- Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP.Nucleic acids research · 2009Article
- Probing the functional impact of sequence variation on p53-DNA interactions using a novel microsphere assay for protein-DNA binding with human cell extracts.PLoS genetics · 2009Article
- A survey of genomic properties for the detection of regulatory polymorphisms.PLoS computational biology · 2007Article
- Identification of polymorphic antioxidant response elements in the human genome.Human molecular genetics · 2007Article
- Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations.BMC genomics · 2006Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOver 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be associated with a cell phenotype. These functional SNPs are consequently important in understanding human health. Information related to functional SNPs in candidate disease genes is critical for cost effective genetic association studies, which attempt to understand the genetics of complex diseases like diabetes, Alzheimer's, etc. Robust methods for the identification of functional SNPs are therefore crucial. We report one such experimental approach.
resultsSequence conserved between mouse and human genomes, within 5 kilobases of the 5-prime end of 176 GPCR genes, were screened for SNPs. Sequences flanking these SNPs were scored for transcription factor binding sites. Allelic pairs resulting in a significant score difference were predicted to influence the binding of transcription factors (TFs). Ten such SNPs were selected for mobility shift assays (EMSA), resulting in 7 of them exhibiting a reproducible shift. The full-length promoter regions with 4 of the 7 SNPs were cloned in a Luciferase based plasmid reporter system. Two out of the 4 SNPs exhibited differential promoter activity in several human cell lines.
conclusionsWe propose a method for effective selection of functional, regulatory SNPs that are located in evolutionary conserved 5-prime flanking regions (5'-FR) regions of human genes and influence the activity of the transcriptional regulatory region. Some SNPs behave differently in different cell types.
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