Center for Human and Clinical Genetics Leiden University Medical Center Genetic variation databases

SNP Databases 

• ALFRED - The ALlele FREquency Database
• CGAP SNP index
• CHIP Bioinformatics Portal
• dbSNP <=> Refseq
• dbSNP - Database of Single Nucleotide Polymorphisms
• dbQSNP - A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.
• FESD - Functional element SNP database
• Forensic SNP Information
• F-SNP - functional SNPs, specifically prioritized for disease association studies
• Gene Viewer - displays SNPs in mRNA sequences
• GeneSNPs - 
• Glovar - Glovar shows sequence variation in a genomic context (EnsEMBL/Sanger)
• HGVBASE - Human Genic Bi Allelic SEquences
• International HapMap Project
• Japanese SNP Database
• Mouse SNP database
• PhenCode - variants from locus-specific databases displayed in the UCSC genome browser
• SNAP - a SNP annotation platform
• SNP@WEB - a web-based catalog of databases and tools for SNP studies.
• SNP500Cancer Database -
• SNPpipe - SNP selection pipeline
• SNPper Retrieve known SNPs by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions.
• SNPseek - Retrieval and Analysis of Functionally Relevant SNPs
• Tagger - tool for the selection and evaluation of tag SNPs from genotype data
• The SNP Consortium Home Page
• TopoSNP database - visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and display of geometric and relative entropy calculations
• UW-FHCRC Variation Discovery Resource

SNP-specific primer design software

• Pira-PCR - PCR Primer design for restriction analysis of single nucleotide polymorphisms
• SNAP - Snap provides tools for designing sequence primers and evaluating RNA splicing effects

SNP detection and effect prediction

• PolyPhen: prediction of functional effect of human nsSNPs
• PupaSuite - an interactive web-based SNP analysis tool that allows for the selection of relevant SNPs within a gene
• SNPeffect - a database containing information on SNPs and their effects on protein stability and aggregation.
• snp2prot: A tool to map human DNA variation onto proteins.

Copy number variation databases

• Chromosome Abnormality Database - an on-line collection of constitutional abnormal karyotypes
• Database of Genomic Variants - A curated catalogue of large-scale variation in the human genome
• DECIPHER - DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources
• ECARUCA - European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations
• Human Structural Variation Database - Copy number variation database (Eichler lab)
• The Chromosome Anomaly Collection - contains examples of unbalanced chromosome abnormalities (UBCAs) without phenotypic effect
• CNV Project - The Copy Number Variation (CNV) Project Data Index
• Structural Genome Variation Nature Genetics 39(7s)(2007) Supplement highlighting recent advances in human genomic variation

Disease-causing variations

• Mutation database list List of disease-causing variation databases

Sequence variation nomenclature

• HGVS guidelines - Sequence variation nomenclature guidelines of the Human Genome Variation Society
• Mutalyzer - a tool to check sequence variation descriptions
• Mutation Checker v.3 - a tool to verify the effects of DNA level sequence variation

SNP Discovery tools

• novoSNP is a program that will help you find variations (SNPs and short INDELs) in resequencing projects.
• Polybayes - a computer program for the automated analysis of single-nucleotide polymorphism (SNP) discovery in redundant DNA sequences.
• PolyPhred - a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.
• ssahaSNP - a polymorphism detection tool that detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence.

   

Polymorphic microsatellite markers

• TPMD - Taiwan Polymorphic Marker Database

If you have any comments or suggestions be sure to let me know!

Peter Taschner

Last modified: November 19, 2008