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 II - 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
• Genome Variation Server - GVS129(hg18)
• Genome Variation Server - GVS131(hg19)
• GWAScentral - a genotype-phenotype association database(formerly HGVBASE)
• International HapMap Project
• Japanese SNP Database
• Mouse SNP query (MGI)
• The database of polymorphic miRNA-target interactions
• PhenCode - variants from locus-specific databases displayed in the UCSC genome browser
• PolymiRTS Polymorphism in microRNA Target Site - a database of naturally occurring DNA variations in predicted and experimentally identified microRNA (miRNA) target sites
• SeattleSNPs - a variation discovery resource
• SNAP - SNP annotation and Proxy Search
• SNP@WEB - a web-based catalog of databases and tools for SNP studies.
• SNP500Cancer Database -
• 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.
• Tagger - tool for the selection and evaluation of tag SNPs from genotype data

SNP-specific primer design software

• Pira-PCR - PCR Primer design for restriction analysis of single nucleotide polymorphisms
• Primo SNP - Tool for designing sequence primers and evaluating RNA splicing effects
• SNPCheckV2 - SNPCheck is a tool for performing batch checks for the presence of SNPs in predicted PCR primer binding sites

SNP detection and effect prediction

• GenEpi Toolbox- tools for the evaluation and prediction of genetic-epidemiological data including human SNPs
• pfSNP- Potentially functional SNP Search Engine
• PolyPhen-2- prediction of functional effects of human nsSNPs
• PupaSuite - an interactive web-based SNP analysis tool that allows for the selection of relevant SNPs within a gene
• SNAP- evaluating effects of single amino acid substitutions on protein function.
• snp2prot- A tool to map human DNA variation onto proteins.

Copy number variation databases

• 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, 2004)
• 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

SNP Discovery tools

• novoSNP is a program that will help you find variations (SNPs and short INDELs) in resequencing projects.
• PolyScan - de novo indel detection and SNP identification in the context of high-throughput medical sequencing.
• 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.
• SomaticSniper – WashU somatic SNV detection algorithm for whole genome resequencing data.
• VarScan – Somatic and germline variant detection for massively parallel sequencing

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

Peter Taschner

Last modified: January 11, 2012