SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions

BMC Bioinformatics. 2008;9 Suppl 1(Suppl 1):S2. doi: 10.1186/1471-2105-9-S1-S2.


Background: Analysis 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.

Description: We 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.

Conclusion: We 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chromosome Mapping / methods*
  • DNA Mutational Analysis / methods
  • Database Management Systems*
  • Databases, Genetic*
  • Genome, Human / genetics*
  • Humans
  • Information Storage and Retrieval / methods
  • Molecular Sequence Data
  • Polymorphism, Single Nucleotide / genetics*
  • Promoter Regions, Genetic / genetics*
  • RNA, Untranslated / genetics
  • Regulatory Elements, Transcriptional / genetics
  • Sequence Analysis, DNA / methods*


  • RNA, Untranslated