SNPselector & High Quality SNP Database
Center for Human Genetics, DUMC
SNPselector will be retired from public use on September 30, 2010
This is the HQSNP DB (high-quality SNP database) developed by the CHG bioinformatics group. A 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 .
A SNP selection tool (SNPselector) is built upon HQSNP. It takes a snp ID list, a gene name list, or a genome region list as input and searches SNPs for genome scans or gene association studies. It can 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 can also take an optional Illumina SNP pre-score file as input to select SNP for Illumina SNP assay. It generates result sorted by tag SNP in LD block, SNP quality, SNP function, SNP regulatory potential, and SNP mutation risk.
User Instruction (manual)
There are four kinds of SNP searches 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 an 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.
For each gene, the program takes about 1 mins to generate the SNP list. Please be patient when you submit a long list of genes or genome regions.
For ABI upload file, please use the exported ABI text file.
For Illumina upload file, please use the original Illumina csv file they send back to you after running their SNP scoring program.
(03/12/05): Now a user can set r2 and MAF (minor allele frequency) value for LD selection. The default values for r2 and MAF are 0.7 and 0.05, respectively.
(03/20/05): Now a user can upload a list of SNP rs# (see the example file - tag.txt) as user defined tag SNPs for LD selection. It's useful when the user has already typed a set of SNPs and wants to use them as tag SNPs to define LD bin.
(07/19/05): The selection of race, r2, and minor allele frequency (MAF) for LD bin analysis has been added to the gene or genomic region level. Please see the table below to find the number code for available genotyping races in SNPselector. Please also check the example files (
gene.txt,loca.txt, spac.txt) for searching SNPs within gene or genomic region. For example, in the "gene.txt", the race number "9" for gene "ACE" means that the LD selected population is "Perlegen African American".
New (12/12/07): The user MUST limit the segment size in the
function "Get genome scan SNPs by genome regions" to 1Mb to get a
response from the server. If the user requires information on a larger
segment, it is suggested that the user submit 1Mb or smaller segments
overlapping by at least 100Kb and integrate the separate results.
||All Caucasian (HapMap Caucasian, Perlegen Caucasian)
||All African (HapMap African, Perlegen African American)
||All Asian (HapMap Chinese & Japanese, Perlegen Chinese)
||Perlegen African American
Search (Human Genome: NCBI build 36.2)
Last Modified: $Date: Fri Dec 14
10:37:33 EST 2007$