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New
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New version of the data
source in this release
for the species
New
source
New data source in this
release for the species
Provides phenotype data Source which provides
phenotype association data
The source contains only
germline data
The source contains only
somatic data
The source contains both
germline and somatic data

Ensembl Variation - Sources Documentation

List of Variation sources for each species - Ensembl 75


Homo sapiens Homo sapiens

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP Variation
Archive dbSNP 138 Former variants names imported from dbSNP Variation synonym
LSDB - Variants dbSNP annotates as being from LSDBs Variation synonym
PubMed - Variants with pubmed citations -
PhenCode - PhenCode is a collaborative project to better understand the relationship between genotype and phenotype in humans Variation,
Variation synonym,
Structural variation
-
ESP 6500 The goal of the NHLBI GO Exome Sequencing Project is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by sequencing the protein coding regions of the human genome across diverse, richly-phenotyped populations Variation,
Variation synonym
New
version
HGMD-PUBLIC 2013.3 Variants from HGMD-PUBLIC dataset September 2013 Variation,
Phenotype
New
version
Provides phenotype data
DGVa 01/2014 Database of Genomic Variants Archive Structural variation,
Phenotype,
Study
New
version
Provides phenotype data
NHGRI_GWAS_catalog 10/12/2013 Variants associated with phenotype data from the NHGRI GWAS catalog Phenotype,
Study
New
version
Provides phenotype data
EGA 12/2013 Variants imported from the European Genome-phenome Archive with phenotype association Study
New
version
Uniprot 11/12/2013 Variants with protein annotation imported from Uniprot Variation synonym,
Phenotype,
Study
New
version
Provides phenotype data
OMIM 17/12/2013 Variations linked to entries in the Online Mendelian Inheritance in Man (OMIM) database Phenotype,
Study
New
version
Provides phenotype data
Open Access GWAS DB - Johnson & O'Donnell 'An Open Access Database of Genome-wide Association Results' PMID:19161620 Phenotype,
Study
Provides phenotype data
COSMIC 67 Somatic mutations found in human cancers from the COSMIC project Variation,
Phenotype
Provides phenotype data
dbSNP_ClinVar 30/12/2013 Variants of clinical significance imported from dbSNP/ClinVar Variation,
Phenotype
New
version
Provides phenotype data
DDG2P 07/11/2013 Developmental Disorders Genotype-to-Phenotype Database Phenotype
New
version
Provides phenotype data
GIANT 2010 The Genetic Investigation of ANthropometric Traits (GIANT) consortium is an international collaboration that seeks to identify genetic loci that modulate human body size and shape, including height and measures of obesity Phenotype Provides phenotype data
OMIMGENE - Online Mendelian Inheritance in Man (OMIM) database Phenotype Provides phenotype data
Orphanet 22/10/2013 The portal for rare diseases and drugs Phenotype Provides phenotype data
MAGIC 2010 MAGIC (the Meta-Analyses of Glucose and Insulin-related traits Consortium) represents a collaborative effort to combine data from multiple GWAS to identify additional loci that impact on glycemic and metabolic traits Phenotype Provides phenotype data
dbGaP - The database of Genotypes and Phenotypes. Phenotype,
Study
Provides phenotype data
AMDGC 1 The AMD Gene consortium is an international collaboration that seeks to identify genetic loci associated with age-related macular degeneration . Phenotype,
Study
Provides phenotype data
GEFOS 1 The GEnetic Factors for OSteoporosis Consortium international collaboration that seeks to identify common risk gene variants for osteoporosis Phenotype Provides phenotype data
IIBDGC 1 International Inflammatory Bowel Disease Genetics Consortium Phenotype Provides phenotype data
Teslovich 1 Biological, clinical and population relevance of 95 loci for blood lipids Phenotype Provides phenotype data

Chip SourceVersionDescriptionData type(s) Otherinfo
Illumina_CytoSNP12v1 - Variants from the Illumina Cyto SNP-12 v1 whole genome SNP genotyping chip designed for cytogenetic analysis Structural variation
Illumina_Human660W-quad - Variants from the Illumina Human 660W-Quad whole genome SNP genotyping chip designed for association studies Structural variation
Illumina_Human1M-duoV3 - Variants from the Illumina Human 1M-DuoV3 whole genome SNP genotyping chip designed for association studies Structural variation
Affy GenomeWideSNP_6 CNV - Copy Number Variation (CNV) probes from the Affymetrix Genome-Wide Human SNP Array 6.0 Structural variation

LSDB SourceVersionDescriptionData type(s) Otherinfo
dbPEX - dbPEX, PEX Gene Database Variation synonym
KAT6BDB - K(lysine) acetyltransferase 6B database, BCM Variation synonym
LSDB_PPIB 17/02/2011 PPIB homepage - Osteogenesis Imperfecta Variant Database - Leiden Open Variation Database Variation synonym
LSDB_CRTAP 08/04/2011 CRTAP homepage - Osteogenesis Imperfecta Variant Database - Leiden Open Variation Database Variation synonym
LSDB_LEPRE1 08/04/2011 LEPRE1 homepage - Osteogenesis Imperfecta Variant Database - Leiden Open Variation Database Variation synonym
LSDB_FKBP10 16/05/2011 FKBP10 homepage - Osteogenesis Imperfecta Variant Database - Leiden Open Variation Database Variation synonym
HbVar - A Database of Human Hemoglobin Variants and Thalassemias Variation synonym
LMDD - Leiden Muscular Dystrophy Database Variation synonym
OIVD - Osteogenesis Imperfecta Variant Database Variation synonym
PAHdb - Phenylalanine hydroxylas database Variation synonym
Infevers - The registry of Hereditary Auto-inflammatory Disorders Mutations Variation synonym

Others species

Bos taurus Bos taurus

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
Archive dbSNP 138 Former variants names imported from dbSNP Variation synonym
DGVa 04/2013 Database of Genomic Variants Archive Structural variation,
Study
PubMed - Variants with pubmed citations Study
Animal_QTLdb 03/10/2012 The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and association data on livestock animal species Phenotype,
Study
Provides phenotype data
OMIA 24/09/2013 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype Provides phenotype data

Canis familiaris Canis familiaris

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP Variation
New
version
Archive dbSNP 139 Former variants names imported from dbSNP Variation synonym
New
source
DGVa 06/2012 Database of Genomic Variants Archive Structural variation
New
version
OMIA 02/01/2014 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype
New
version
Provides phenotype data

Danio rerio Danio rerio

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
Archive dbSNP 138 Former variants names imported from dbSNP Variation synonym
DGVa 10/2013 Database of Genomic Variants Archive Structural variation,
Study
OMIA - Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype Provides phenotype data
ZFIN 22/07/2013 The zebrafish model organism database Phenotype Provides phenotype data

Drosophila melanogaster Drosophila melanogaster

SourceVersionDescriptionData type(s) Otherinfo
DPGP 1 Variation features from DPGP, with Ensembl identifiers Variation

Equus caballus Equus caballus

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
New
version
Archive dbSNP 139 Former variants names imported from dbSNP Variation synonym
New
version
DGVa 06/2012 Database of Genomic Variants Archive Structural variation,
Study
OMIA 02/01/2014 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype
New
version
Provides phenotype data

Felis catus Felis catus

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 127 Variants (including SNPs and indels) imported from dbSNP [remapped from build CAT] Variation,
Variation synonym
OMIA - Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype Provides phenotype data

Gallus gallus Gallus gallus

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
Archive dbSNP 138 Former variants names imported from dbSNP Variation synonym
OMIA - Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype Provides phenotype data

Macaca mulatta Macaca mulatta

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
DGVa 11/2012 Database of Genomic Variants Archive Structural variation,
Study
OMIA - Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype Provides phenotype data

Meleagris gallopavo Meleagris gallopavoNew species!

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
New
source
Archive dbSNP 139 Former variants names imported from dbSNP Variation synonym
New
source
OMIA - Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype
New
source
Provides phenotype data

Monodelphis domestica Monodelphis domestica

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
New
version

Mus musculus Mus musculus

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP Variation
Archive dbSNP 138 Former variants names imported from dbSNP Variation synonym
DGVa 12/2013 Database of Genomic Variants Archive Structural variation,
Study
New
version
PubMed - Variants with pubmed citations Study
EuroPhenome - EuroPhenome Phenotype Provides phenotype data
MGP - WTSI Mouse Genetics Project Phenotype Provides phenotype data

Nomascus leucogenys Nomascus leucogenys

SourceVersionDescriptionData type(s) Otherinfo
ENSEMBL - Variants for northern white-cheeked gibbon genome of a wild-born female named 'Asia' called by ENSEMBL pipeline Variation
dbSNP - Variants submitted to dbSNP Variation synonym

Ornithorhynchus anatinus Ornithorhynchus anatinus

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
New
version
Ensembl 1 Original names assigned prior to dbSNP submission Variation synonym
New
source

Ovis aries Ovis aries

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
IlluminaOvineSNP50 - Illumina OvineSNP50 BeadChip Variation
OMIA - Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype Provides phenotype data
IllumniaOvineHDSNP - Illumnia Ovine Infinium HD SNP BeadChip Variation

Pan troglodytes Pan troglodytes

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
OMIA - Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species (other than human and mouse) Phenotype Provides phenotype data

Pongo abelii Pongo abelii

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP Variation

Rattus norvegicus Rattus norvegicus

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
Archive dbSNP 138 Former variants names imported from dbSNP Variation synonym
PubMed - Variants with pubmed citations -
ENSEMBL:celera - Variants from Celera called by the ENSEMBL pipeline Variation synonym
ENSEMBL:STAR-4strain - Variants in STAR-4strain called by the ENSEMBL pipeline Variation synonym
ENSEMBL:STAR-gtype - Variants in STAR-gtype called by the ENSEMBL pipeline Variation synonym
ENSEMBL:RNB1 - Variants in RNB1 called by the ENSEMBL pipeline Variation synonym
PubMed - Variants with pubmed citations -
RGD 04/01/2013 QTLs from the Rat Genome Database (RGD) Phenotype Provides phenotype data

Saccharomyces cerevisiae Saccharomyces cerevisiae

SourceVersionDescriptionData type(s) Otherinfo
SGRP - Variation features from SGRP, with Ensembl identifiers Variation

Sus scrofa Sus scrofa

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
Archive dbSNP 138 Former variants names imported from dbSNP Variation synonym
Pig SNP Consortium 0 PorcineSNP60 BeadChip Variation,
Variation synonym
Animal_QTLdb - The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and association data on livestock animal species Phenotype,
Study
Provides phenotype data
DGVa 12/2013 Database of Genomic Variants Archive Structural variation,
Study
New
version

Taeniopygia guttata Taeniopygia guttata

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP Variation,
Variation synonym
New
version
Archive dbSNP 139 Former variants names imported from dbSNP Variation synonym
New
version

Tetraodon nigroviridis Tetraodon nigroviridis

SourceVersionDescriptionData type(s) Otherinfo
dbSNP 132 Variants (including SNPs and indels) imported from dbSNP and mapped to the TETRAODON 8.0 assembly Variation,
Variation synonym
Archive dbSNP 132 Former variants names imported from dbSNP Variation synonym