This section collects together tools that help identifying and annotation of SNPs. In addition some of them can be used to map SNPs to genes.
CandiSNPer is a tool that determines the LD region around a significant SNP from a GWAS. It provides a list with functional annotation and LD values for the SNPs found in the LD region. This tool can be used to map SNPs to genes also.
According to Karchin et al. MutaGenesys is a tool that identifies inderect correlations between SNPs and mutations from OMIM. MutaGeneSys uses genome-wide genotype data to estimate disease susceptibility. Our system integrates three data sources: the International HapMap project, whole-genome marker correlation data and the Online Mendelian Inheritance in Man (OMIM) database. It accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete.
MutationTagger is a rule- and regular expression-based approach that allows for the retrieval of protein point mutations from the whole PubMed database specifically for any given protein.
PolySearch is a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.
Snap is a server designed to analyze single genes and relationships between genes basing on SNPs in human genome. Several public databases are integrated.
In addition to other functions of this program, it can be used to seach related genes of SNP by giving the rs-code as an input. This way program provides info about chromosome number, position, alleles, gene, feature left and right neighbour genes.
MedRefSNP
database provides integrated information about SNPs collected from the
PubMed and OMIM databases. The RefSNP identifiers are automatically
identified and are linked to various information sources such as the
dbSNP, the HapMap database, the Entrez Gene database, the UCSC genome
browser, the CGAP Pathway Searcher, and genetic association databases.
And, each SNP is checked to determine whether the PolyDoms, SNPs3D or
PolyPhen databases predicts that the SNP affects the phenotype of the
protein encoded by the gene carrying the SNP. Also, neighboring SNPs
showing strong linkage disequilibrium (LD) with published SNPs are
included, using HapMap data
Varietas is a web-based database portal that has been designed to aid researchers to easily retrieve information on a set of variations (eg. SNPs and CNVs), related genes and genomic elements in a batch like manner. As an input user can give variety of different features such as SNPs, genes, keywords or locations, or any combinations of them. These inputs are queried against VarietasDB that contain integrated data from various biological databases (including Ensembl, dbSNP, GAD, SNPedia).
WGAViewer is a free software tool that is designed to provide a user-friendly interface to annotate, visualize, and help interpret the full set of P values indicating evidence of association resulting from a Whole Genome Association (WGA) study. Current version offers six classes of annotation: 1. Chromosome view of WGA results, 2. Genic annotation of WGA results, 3. Annotation for SNPs, 4. Gene/SNP finding , 5. Evidence from multiple genome scans and 6. supporting/QC databases.