Abstract
BackgroundAnalysis of single nucleotide polymorphism (SNP) is becoming a key research in genomics fields. Many functional analyses of SNPs have been carried out for coding regions and splicing sites that can alter proteins and mRNA splicing. However, SNPs in non-coding regulatory regions can also influence important biological regulation. Presently, there are few databases for SNPs in non-coding regulatory regions.DescriptionWe identified 488,452 human SNPs in the putative promoter regions that extended from the +5000 bp to -500 bp region of the transcription start sites. Some SNPs occurring in transcription factor (TF) binding sites were also predicted (47,832 SNP; 9.8%). The result is stored in a database: SNP@promoter. Users can search the SNP@Promoter database using three entries: 1) by SNP identifier (rs number from dbSNP), 2) by gene (gene name, gene symbol, refSeq ID), and 3) by disease term. The SNP@Promoter database provides extensive genetic information and graphical views of queried terms.ConclusionWe present the SNP@Promoter database. It was created in order to predict functional SNPs in putative promoter regions and predicted transcription factor binding sites. SNP@Promoter will help researchers to identify functional SNPs in non-coding regions.
Highlights
Analysis of single nucleotide polymorphism (SNP) is becoming a key research in genomics fields
It was created in order to predict functional SNPs in putative promoter regions and predicted transcription factor binding sites
After finishing the Human Genome Project, biologists' interest has shifted to non-repetitive sequence variants in genome, by far the most common of which are single nucleotide polymorphisms (SNPs)
Summary
After finishing the Human Genome Project, biologists' interest has shifted to non-repetitive sequence variants in genome, by far the most common of which are single nucleotide polymorphisms (SNPs). More than 99% of human DNA sequences are the same across all populations, some SNPs can have a major impact on how humans respond to diseases; environmental insults such as bacteria, viruses, toxins, and chemicals; and drugs and other therapies. This makes SNPs of great value for biomedical research and for developing pharmaceutical products and for medical diagnostics. Many functional studies of SNPs were focused on SNPs located in coding regions that can influence phenotype by altering the encoded proteins [9,10] They can influence premature termination that can cause nonsense-mediated mRNA decay (NMD) [11]. Platform for biologists including disease associated genes, transcription factor binding sites, and a graphic viewer
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