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Short variations—SNVs, short indels
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1000 Genomes
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http://www.1000genomes.org
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Human short variants and inferred genotypes
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dbSNP
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http://www.ncbi.nlm.nih.gov/projects/SNP
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Short variants from all species
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HapMap
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http://www.hapmap.org
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Human short variants and population group haplotypes
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Structural variations—structural rearrangements, CNVs, large indels
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dbVar
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http://www.ncbi.nlm.nih.gov/dbvar
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Structural variants from all species
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DGV
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http://projects.tcag.ca/variation
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Structural variants from healthy human controls
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DGVa
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http://www.ebi.ac.uk/dgva
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Structural variants from all species
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General variants associated with phenotypes
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ClinVar
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http://www.ncbi.nlm.nih.gov/clinvar
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Human variant–disease associations (in development)
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HGMD
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http://www.hgmd.org
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Human variant–disease associations (inherited diseases)
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OMIM
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http://www.omim.org
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Human variant–disease associations (includes extensive gene and phenotype descriptions)
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SwissVar
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http://swissvar.expasy.org
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Human variant–disease associations (non-synonymous SNVs only)
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GWAS and other association studies
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dbGaP
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http://www.ncbi.nlm.nih.gov/gap
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Controlled access to individual genotype/phenotype data from association studies
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EGA
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http://www.ebi.ac.uk/ega
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Controlled access to individual genotype/phenotype data from association studies
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GAD
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http://geneticassociationdb.nih.gov
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Mainly complex disease SNVs from association studies
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NHGRI GWAS Catalog
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http://www.genome.gov/gwastudies
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Significant SNVs from GWAS
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Cancer genes and variants
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ICGC
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http://www.icgc.org
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Somatic variants from tumor sequencing projects
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COSMIC
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http://sanger.ac.uk/genetics/CGP/cosmic
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Somatic variants from tumor sequencing and literature
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Cancer Gene Census
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http://sanger.ac.uk/genetics/CGP/Census
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Comprehensive list of cancer-related genes
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Cancer Gene Index
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http://ncicb.nci.nih.gov/NCICB/projects/cgdcp
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Comprehensive list of cancer-related genes, including gene–disease and gene–drug relationships
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TCGA
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http://cancergenome.nih.gov
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Somatic variants from tumor sequencing projects
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Pharmacogenomic genes and variants
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DrugBank
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http://drugbank.ca
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Drug properties and protein amino acid target sequences
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PharmGKB
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http://www.pharmgkb.org
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Curated and text-mined variant–drug response associations
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Crowdsourced genes and variants
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Gene Wiki
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http://en.wikipedia.org/wiki/Portal:Gene_Wiki
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Human gene/protein annotations
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SNPedia
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http://www.snpedia.com
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Human SNV–disease associations
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WikiGenes
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https://www.wikigenes.org
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Gene annotations from all species
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Viewers of the structural and functional impact of variants
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DMDM
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http://bioinf.umbc.edu/dmdm
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Aggregates human protein mutations at individual domain positions
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LS-SNP/PDB
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http://ls-snp.icm.jhu.edu/ls-snp-pdb
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Variant/PDB structure viewer (includes multiple filters for selection of variants)
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MutDB
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http://mutdb.org
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Variant/PDB structure viewer (includes SIFT predictions for nonsynonymous mutations)
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SAAPdb
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http://bioinf.org.uk/saap/db
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Variant/PDB structure viewer (includes impact on physico-chemical and functional features)
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StSNP
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http://ilyinlab.org/StSNP
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Variant/PDB structure viewer (includes physico-chemical impact for nonsynonymous mutations)
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SNPeffect
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http://snpeffect.vib.be
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Variant/PDB structure viewer (includes predictions for variants to cause protein aggregation)
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TopoSNP
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http://gila-fw.bioengr.uic.edu/snp/toposnp
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Variant/PDB structure viewer (includes location of variant on surface, in pocket or in core)
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