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New version of the data
source in this release
for the species
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
Data types - variants count:
greater than 1 million
from 1,000 to 999,999
less than 1,000

Ensembl Variation - Sources Documentation

List of Variation sources for each species - Ensembl 78

Homo sapiens Homo sapiens
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP (mapped to GRCh38)
Variation
> 62 million
Link
Archive dbSNP 138 Former variants names imported from dbSNP
Synonym
> 10 million
Link
AMDGC 1 The AMD Gene consortium is an international collaboration that seeks to identify genetic loci associated with age-related macular degeneration .
Phenotype
> 3,000
Link
Study
Provides phenotype data
ClinVar 10/2014 Variants of clinical significance imported from ClinVar
Variation
> 9,000
Link
Phenotype
> 103,000
Link
Provides phenotype data
COSMIC 71 Somatic mutations found in human cancers from the COSMIC project
Variation
> 2 million
Link
Phenotype
> 2 million
Link
Provides phenotype data
dbGaP 05/2014 The database of Genotypes and Phenotypes.
Phenotype
> 41,000
Link
Study
Provides phenotype data
DDG2P 18/07/2014 Developmental Disorders Genotype-to-Phenotype Database
Phenotype
> 2,000
Link
Provides phenotype data
DGVa 10/2014 Database of Genomic Variants Archive
SV
> 3 million
Link
Phenotype
> 73,000
Link
Study
Provides phenotype data
EGA 10/2014 Variants imported from the European Genome-phenome Archive with phenotype association
Study
ESP 09/05/2014 Data from NHLBI ESP version v.0.0.28. 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
Variation
> 106,000
Link
Synonym
668
Link
GEFOS 1 The GEnetic Factors for OSteoporosis Consortium international collaboration that seeks to identify common risk gene variants for osteoporosis
Phenotype
> 1,000
Link
Provides phenotype data
GIANT 1 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
> 7,000
Link
Provides phenotype data
HGMD-PUBLIC 2014.2 Variants from HGMD-PUBLIC dataset June 2014 (mapped to GRCh38)
Variation
> 97,000
Link
Phenotype
> 96,000
Link
Provides phenotype data
IIBDGC 1 International Inflammatory Bowel Disease Genetics Consortium
Phenotype
> 10,000
Link
Provides phenotype data
LSDB - Variants dbSNP annotates as being from LSDBs
Synonym
> 88,000
Link
MAGIC 1 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
> 1,000
Link
Provides phenotype data
NHGRI_GWAS_catalog 15/10/2014 Variants associated with phenotype data from the NHGRI GWAS catalog
Phenotype
> 19,000
Link
Study
Provides phenotype data
OMIM 16/10/2014 Variations linked to entries in the Online Mendelian Inheritance in Man (OMIM) database
Phenotype
> 17,000
Link
Study
Provides phenotype data
OMIMGENE 02/06/2014 Online Mendelian Inheritance in Man (OMIM) database
Phenotype
> 5,000
Link
Provides phenotype data
Orphanet 25/06/2014 The portal for rare diseases and drugs
Phenotype
> 5,000
Link
Provides phenotype data
PhenCode 30/04/2014 PhenCode is a collaborative project to better understand the relationship between genotype and phenotype in humans
Variation
> 26,000
Link
Synonym
883
Link
-
Teslovich 1 Biological, clinical and population relevance of 95 loci for blood lipids
Phenotype
> 7,000
Link
Provides phenotype data
Uniprot 01/10/2014 Variants with protein annotation imported from Uniprot
Synonym
> 38,000
Link
Phenotype
> 3,000
Link
Study
Provides phenotype data
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Affy GenomeWideSNP_6 CNV - Copy Number Variation (CNV) probes from the Affymetrix Genome-Wide Human SNP Array 6.0
SV
> 945,000
Link
HumanCoreExome-12 1 Variants from the Illumina HumanCoreExome-12 v1 genotyping chip.
Variation
> 27,000
Link
Set
> 534,000
Link
Illumina_CytoSNP12v1 1 Variants from the Illumina Cyto SNP-12 v1 whole genome SNP genotyping chip designed for cytogenetic analysis
SV
496
Link
Set
> 51,000
Link
Illumina_Human1M-duo 3 Variants from the Illumina Human 1M-Duo v3 whole genome SNP genotyping chip designed for association studies
SV
> 35,000
Link
Set
> 1 million
Link
Illumina_Human660W-quad - Variants from the Illumina Human 660W-Quad whole genome SNP genotyping chip designed for association studies
SV
> 64,000
Link
Set
> 590,000
Link
Affy GenomeWideSNP_6.0 - Variants from the Affymetrix Genome-Wide Human SNP Array 6.0
Set
> 935,000
Link
Affy GeneChip 500K - Variants from the Affymetrix GeneChip Human Mapping 500K Array Set
Set
> 495,000
Link
Illumina_Cardio-Metabo_Chip - Variants from the Illumina Cardio-Metabo_Chip genotyping array designed to target variants of interest for metabolic and cardiovascular disease traits
Set
> 196,000
Link
Illumina_HumanOmni1-Quad - Variants from the Illumina HumanOmni1-Quad whole genome genotyping array designed for association studies
Set
> 1 million
Link
Illumina_HumanHap650Y - Variants from the Illumina HumanHap650Y v3.0 whole genome genotyping array designed for association studies
Set
> 660,000
Link
Illumina_HumanOmni2.5 - Variants from the Illumina HumanOmni2.5 4v1 whole genome genotyping array designed for association studies
Set
> 2 million
Link
Illumina_Human610_Quad - Variants from the Illumina Human610_Quad v1_B whole genome genotyping array designed for association studies
Set
> 599,000
Link
Illumina_HumanHap550 - Variants from the Illumina Human550 v3.0 whole genome genotyping array designed for association studies
Set
> 561,000
Link
Illumina_HumanOmni5 - Variants from the Illumina HumanOmni5v1 whole genome genotyping array designed for association studies
Set
> 4 million
Link
Illumina_ExomeChip - Variants from the Illumina ExomeChip genotyping array designed to target variants within exons
Set
> 297,000
Link
Illumina_ImmunoChip - Variants from the Illumina ImmunoChip genotyping array designed to target variants of interest for autoimmune and inflammatory diseases
Set
> 188,000
Link
HumanOmniExpress - Variants from the Illumina HumanOmniExpress 12v1-1_a whole genome genotyping array
Set
> 719,000
Link
LSDB SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbPEX - dbPEX, PEX Gene Database
Synonym
147
Link
HbVar - A Database of Human Hemoglobin Variants and Thalassemias
Synonym
> 1,000
Link
Infevers - The registry of Hereditary Auto-inflammatory Disorders Mutations
Synonym
618
Link
KAT6BDB - K(lysine) acetyltransferase 6B database, BCM
Synonym
19
Link
LMDD - Leiden Muscular Dystrophy Database
Synonym
678
Link
OIVD - Osteogenesis Imperfecta Variant Database
Synonym
779
Link
PAHdb - Phenylalanine hydroxylas database
Synonym
541
Link

Others species

Bos taurus Bos taurus
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 140 Variants (including SNPs and indels) imported from dbSNP
Variation
> 73 million
Link
Archive dbSNP 140 Former variants names imported from dbSNP
Synonym
> 151,000
Link
Animal_QTLdb 25/08/2014 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
> 11,000
Link
Study
Provides phenotype data
DGVa 05/2014 Database of Genomic Variants Archive
SV
> 2,000
Link
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
87
Link
Provides phenotype data
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Illumina BovineSNP50 BeadChip - Variants from the Illumina BovineSNP50 BeadChip genotyping array
Set
> 56,000
Link
Illumina BovineLD BeadChip - Variants from the Illumina BovineLD BeadChip genotyping array
Set
> 7,000
Link
Illumina BovineHD BeadChip - Variants from the Illumina BovineHD BeadChip genotyping array
Set
> 780,000
Link
Canis familiaris Canis familiaris
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
> 3 million
Link
Archive dbSNP 139 Former variants names imported from dbSNP
Synonym
> 69,000
Link
DGVa 05/2014 Database of Genomic Variants Archive
SV
470
Link
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
180
Link
Provides phenotype data
Danio rerio Danio rerio
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP
Variation
> 1 million
Link
Synonym
Archive dbSNP 138 Former variants names imported from dbSNP
Synonym
> 33,000
Link
DGVa 05/2014 Database of Genomic Variants Archive
SV
> 5,000
Link
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
3
Link
Provides phenotype data
ZFIN 22/07/2013 The zebrafish model organism database
Phenotype
> 30,000
Link
Provides phenotype data
Drosophila melanogaster Drosophila melanogaster
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
DPGP 1 Variation features from DPGP, with Ensembl identifiers
Variation
> 6 million
Link
Equus caballus Equus caballus
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
> 4 million
Link
Archive dbSNP 139 Former variants names imported from dbSNP
Synonym
> 4,000
Link
Animal_QTLdb 25/08/2014 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
345
Link
Study
Provides phenotype data
DGVa 05/2014 Database of Genomic Variants Archive
SV
> 193,000
Link
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
33
Link
Provides phenotype data
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Illumina EquineSNP50 BeadChip - Variants from the Illumina EquineSNP50 BeadChip genotyping array
Set
> 54,000
Link
Felis catus Felis catus
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 127 Variants (including SNPs and indels) imported from dbSNP [remapped from build CAT]
Variation
> 327,000
Link
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
39
Link
Provides phenotype data
Gallus gallus Gallus gallus
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 140 Variants (including SNPs and indels) imported from dbSNP
Variation
> 9 million
Link
Archive dbSNP 140 Former variants names imported from dbSNP
Synonym
> 27,000
Link
Animal_QTLdb 25/08/2014 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
> 4,000
Link
Study
Provides phenotype data
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
35
Link
Provides phenotype data
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Affymetrix Chicken600K Array - Variants from the Affymetrix Chicken600K genotyping array
Set
> 577,000
Link
Macaca mulatta Macaca mulatta
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP
Variation
> 3 million
Link
DGVa 05/2014 Database of Genomic Variants Archive
SV
123
Link
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
3
Link
Provides phenotype data
Meleagris gallopavo Meleagris gallopavo
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
> 9,000
Link
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
2
Link
Provides phenotype data
Monodelphis domestica Monodelphis domestica
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
> 1 million
Link
Mus musculus Mus musculus
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP
Variation
> 71 million
Link
Archive dbSNP 138 Former variants names imported from dbSNP
Synonym
> 250,000
Link
DGVa 05/2014 Database of Genomic Variants Archive
SV
> 762,000
Link
Study
EuroPhenome - EuroPhenome
Phenotype
> 3,000
Link
Provides phenotype data
IMPC 26/06/2014 International Mouse Phenotyping Consortium
Phenotype
649
Link
Provides phenotype data
Nomascus leucogenys Nomascus leucogenys
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
ENSEMBL - Variants for northern white-cheeked gibbon genome of a wild-born female named 'Asia' called by ENSEMBL pipeline
Variation
> 1 million
Link
Ornithorhynchus anatinus Ornithorhynchus anatinus
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
> 1 million
Link
Ensembl 1 Original names assigned prior to dbSNP submission
Synonym
> 773,000
Link
Ovis aries Ovis aries
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 140 Variants (including SNPs and indels) imported from dbSNP
Variation
> 32 million
Link
Animal_QTLdb 25/08/2014 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
789
Link
Study
Provides phenotype data
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
49
Link
Provides phenotype data
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
IlluminaOvineHDSNP - Illumnia Ovine Infinium HD SNP BeadChip
Variation
135
Link
Synonym
> 684,000
Link
Set
> 685,000
Link
IlluminaOvineSNP50 - Illumina OvineSNP50 BeadChip
Variation
> 7,000
Link
Synonym
> 48,000
Link
Set
> 54,000
Link
Pan troglodytes Pan troglodytes
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP
Variation
> 1 million
Link
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
1
Link
Provides phenotype data
Pongo abelii Pongo abelii
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP
Variation
> 10 million
Link
Rattus norvegicus Rattus norvegicus
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP
Variation
> 5 million
Link
Archive dbSNP 138 Former variants names imported from dbSNP
Synonym
> 171,000
Link
ENSEMBL:celera - Variants from Celera called by the ENSEMBL pipeline
Synonym
> 2 million
Link
ENSEMBL:RNB1 - Variants in RNB1 called by the ENSEMBL pipeline
Synonym
> 83,000
Link
ENSEMBL:STAR-4strain - Variants in STAR-4strain called by the ENSEMBL pipeline
Synonym
> 125,000
Link
ENSEMBL:STAR-gtype - Variants in STAR-gtype called by the ENSEMBL pipeline
Synonym
> 20,000
Link
RGD 04/01/2013 QTLs from the Rat Genome Database (RGD)
Phenotype
> 1,000
Link
Provides phenotype data
Saccharomyces cerevisiae Saccharomyces cerevisiae
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
SGRP - Variation features from SGRP, with Ensembl identifiers
Variation
> 263,000
Link
Sus scrofa Sus scrofa
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 140 Variants (including SNPs and indels) imported from dbSNP
Variation
> 28 million
Link
Archive dbSNP 140 Former variants names imported from dbSNP
Synonym
> 3,000
Link
Animal_QTLdb 25/08/2014 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
> 11,000
Link
Study
Provides phenotype data
DGVa 05/2014 Database of Genomic Variants Archive
SV
85
Link
Study
Pig SNP Consortium 0 PorcineSNP60 BeadChip
Synonym
> 63,000
Link
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Illumina_PorcineSNP60 - PorcineSNP60 BeadChip
Set
> 63,000
Link
Taeniopygia guttata Taeniopygia guttata
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
> 1 million
Link
Archive dbSNP 139 Former variants names imported from dbSNP
Synonym
> 1,000
Link
Tetraodon nigroviridis Tetraodon nigroviridis
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 132 Variants (including SNPs and indels) imported from dbSNP and mapped to the TETRAODON 8.0 assembly
Variation
> 902,000
Link
Archive dbSNP 132 Former variants names imported from dbSNP
Synonym
956
Link