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Resource:High Quality SNP Database

Name: Resource:High Quality SNP Database
Description: This is the HQSNP DB (high-quality SNP database) developed by CHG bioinformatics group. The high-quality SNP is defined as a SNP having allele frequency or genotyping data. The majority of the HQSNPs come from HapMap, others come from JSNP (Japanese SNP database), TSC (The SNP Consortium), Affymetrix 120K SNP, and Perlegen SNP.

There are four kinds of SNP search you can do:

  • Get SNPs by dbSNP rs#: Choose this search if you have already selected a list of SNPs and you just want to get the SNP information. The program will generate a Excel file containing the SNP flanking sequence, variation, quality, function, etc. In the Excel file, there are 10 highlighted fields. You can send only those highlighted information to Illumina to get SNP pre-score. (The same fields are presented in other types of searches as well.)
  • Get gene SNPs by gene names: Choose this search if you have a list of gene names and you want to get the SNP information in these genes. The gene name can be official gene symbol, Ensembl gene ID, RefSeq accession ID, LocusLink number, etc.
  • Get gene SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get all gene SNP information in these regions. The software will find all the Ensembl genes in the regions and find SNPs associated to each Ensembl gene.
  • Get genome scan SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get evenly spaced SNPs in these regions.
A SNP selection tool (SNPselector) was built upon HQSNP. It took snp ID list, gene name list, or genome region list as input and searched SNPs for genome scan or gene assoctiation study. It could take an optional ABI SNP file (exported from ABI SNP search web page) as input for checking whether the candidate SNP is available from ABI. It could also take an optional Illumina SNP pre-score file as input to select SNP for Illumina SNP assay. It generated results sorted by tag SNP in LD block, SNP quality, SNP function, SNP regulatory potential, and SNP mutation risk. SNPselector is now retired from public use (as of September 30, 2010).
Other Name(s): CHG DAS Data, SNPselector and High Quality SNP Database
Abbreviation: HQSNP DB
Parent Organization: Duke University; North Carolina; USA
Resource Type(s): Web accessible database
Resource: Resource
URL: http://snpselector.duhs.duke.edu/hqsnp36.html
*Id: nif-0000-30254
Keywords: SNP, Genotyping, Data, Allele, Bioinformatics, Genome, Study, Gene
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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Contributors

Aarnaud, Zaidaziz



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Facts about Resource:High Quality SNP DatabaseRDF feed
AbbrevHQSNP DB  +
CurationStatusCurated  +
DefiningCitationhttp://snpselector.duhs.duke.edu/hqsnp36.html  +
DefinitionThis is the HQSNP DB (high-quality SNP dat This is the HQSNP DB (high-quality SNP database) developed by CHG bioinformatics group. The high-quality SNP is defined as a SNP having allele frequency or genotyping data. The majority of the HQSNPs come from HapMap, others come from JSNP (Japanese SNP database), TSC (The SNP Consortium), Affymetrix 120K SNP, and Perlegen SNP.

There are four kinds of SNP search you can do:

  • Get SNPs by dbSNP rs#: Choose this search if you have already selected a list of SNPs and you just want to get the SNP information. The program will generate a Excel file containing the SNP flanking sequence, variation, quality, function, etc. In the Excel file, there are 10 highlighted fields. You can send only those highlighted information to Illumina to get SNP pre-score. (The same fields are presented in other types of searches as well.)
  • Get gene SNPs by gene names: Choose this search if you have a list of gene names and you want to get the SNP information in these genes. The gene name can be official gene symbol, Ensembl gene ID, RefSeq accession ID, LocusLink number, etc.
  • Get gene SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get all gene SNP information in these regions. The software will find all the Ensembl genes in the regions and find SNPs associated to each Ensembl gene.
  • Get genome scan SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get evenly spaced SNPs in these regions.
A SNP selection tool (SNPselector) was built upon HQSNP. It took snp ID list, gene name list, or genome region list as input and searched SNPs for genome scan or gene assoctiation study. It could take an optional ABI SNP file (exported from ABI SNP search web page) as input for checking whether the candidate SNP is available from ABI. It could also take an optional Illumina SNP pre-score file as input to select SNP for Illumina SNP assay. It generated results sorted by tag SNP in LD block, SNP quality, SNP function, SNP regulatory potential, and SNP mutation risk. SNPselector is now retired from public use (as of September 30, 2010).
rom public use (as of September 30, 2010).
Has default formThis property is a special property in this wiki.Resource  +
Has roleWeb accessible database  +
Idnif-0000-30254  +
Is part ofDuke University; North Carolina; USA  +
KeywordsSNP  +, Genotyping  +, Data  +, Allele  +, Bioinformatics  +, Genome  +, Study  +, and Gene  +
LabelResource:High Quality SNP Database  +
ModifiedDate22 June 2011  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
SynonymCHG DAS Data  +, and SNPselector and High Quality SNP Database  +