URL: http://snpinfo.niehs.nih.gov/
Proper Citation: SNPinfo Web Server (RRID:SCR_010589)
Description: SNPinfo Web Server is a set of freely available web-based SNP selection tools where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. SNP Selection and Functional Information *Candidate Gene SNP Selection (GenePipe):SNP selection for candidate genes based on Genome Wide Association Study (GWAS) results, functional SNP prediction and Linkage Disequilibrium (LD) information. *GWAS Functional SNP Selection (GenomePipe):Functional SNP selection from SNPs that are in high LD with GWAS SNPs *GWAS SNP Selection in Linkage Loci (LinkagePipe):GWAS SNP selection in candidate genomic regions (such as linkage loci) *LD TAG SNP Selection (TagSNP):LD tag SNP selection and visualization for single or multiple populations. Finalization of SNP list from various queries. *SNP Function Prediction (FuncPred): Querying SNP function predictions and ethnic-specific allele frequencies. *SNP Information in DNA Sequence (SNPseq):Visualization of SNP related information in the context of DNA sequence. Preparing DNA Sequence for PCR Primer Design considering SNP information. Detailed information of CpG region.
Resource Type: service resource
Defining Citation: PMID:19417063
Keywords: bio.tools
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