Skip to main content

Table 1 Examples of DNA variation databases

From: Systematics for types and effects of DNA variations

Database URL Reference
General variation databases
 Ensembl Variation Database http://www.ensembl.org/info/genome/variation/index.html [17]
ClinVar http://www.ncbi.nlm.nih.gov/clinvar/ [18]
 Database of Short Genetic Variations (dbSNP) http://www.ncbi.nlm.nih.gov/SNP/ [19]
Exome and complete genome sequences
 ExAC http://exac.broadinstitute.org [20]
 NHLBI Exome Sequencing Project (ESP) Exome Variant Server (EVS) http://evs.gs.washington.edu/EVS/ [21]
 The 1000 Genomes Project http://www.internationalgenome.org/ [22]
 European Nucleotide Archive (ENA) https://www.ebi.ac.uk/ena [23]
Locus specific variation databases
 Leiden Open Variation Databases (LOVD) http://www.lovd.nl/3.0/home [24]
 Universal Mutation Database (UMD) http://www.umd.be/ [25]
 ImmunoDeficiency Variation Databases (IDbases) http://structure.bmc.lu.se/idbase [26]
 The TP53 web site http://www.p53.fr/ [48]
Allele frequency databases
 The ALlele FREquency Database (ALFRED) https://alfred.med.yale.edu/alfred/ [27]
 FINDbase http://www.findbase.org/ [28]
 Allele Frequency Net Database (AFND) http://www.allelefrequencies.net/ [29]
 Allele Frequency Community (AFC) http://www.allelefrequencycommunity.org/ [30]
Cancer variation databases
 Catalogue of Somatic Mutations in Cancer (COSMIC) http://cancer.sanger.ac.uk/cosmic [31]
 The Cancer Genome Atlas (TCGA) https://portal.gdc.cancer.gov/ [32]
 International Cancer Genome Consortium (ICGC) https://dcc.icgc.org/ [33]
Ethnic/national databases
 Pakistan Genetic Mutation Database http://www.pakmutation.com/ [34]
 The Singapore Human Mutation And Polymorphism Database http://shmpd.bii.a-star.edu.sg/ [35]
Databases of genomic structural variations
 dbVar https://www.ncbi.nlm.nih.gov/dbvar/content/human_hub/ [36]
 Database of Genomic Variants (DGV) http://dgv.tcag.ca/dgv/ [37]
 Database of Genomic Variants archive (DGVa) https://www.ebi.ac.uk/dgva [38]
 Mitelman Database of Chromosome Aberrations in Cancer http://cgap.nci.nih.gov/Chromosomes/Mitelman  
 Human Polymorphic Inversion Database (InvFEST) http://invfestdb.uab.cat/ [39]
Repeat databases
 The European database of L1-HS retrotransposon insertions in humans (euL1db) http://eul1db.unice.fr/ [40]
 L1base, LINE-1 insertions http://l1base.charite.de/l1base.php [41]
 SINEbase http://sines.eimb.ru/ [42]
 Short Tandem Repeat DNA Internet DataBase (STRBase) https://strbase.nist.gov/ [43]
Methylation databases
 Methylation Bank (MethBank) http://bigd.big.ac.cn/methbank [49]
 NGSmethDB http://bioinfo2.ugr.es:8888/NGSmethDB/ [44]
miRNA target databases
 Polymorphism in microRNAs and their TargetSites (PolymiRTS) http://compbio.uthsc.edu/miRSNP/ [45]
 Somatic mutations altering microRNA-ceRNA interactions (SomamiR DB) http://compbio.uthsc.edu/SomamiR/ [46]
DNA loop database
 R-loop DB http://rloop.bii.a-star.edu.sg/ [47]