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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 10 million
from 1 million to 9.9 million
from 1,000 to 999,999
less than 1,000

Ensembl Variation - Sources Documentation

List of variant sources for each species - Ensembl 81

Human

Human (Homo sapiens)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 142 Variants (including SNPs and indels) imported from dbSNP
Variation
112 million+
Link
Archive dbSNP 142 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 Variation phenotype association data
ClinVar 05/2015 Variants of clinical significance imported from ClinVar
Variation
13,000+
Link
Phenotype
154,000+
Link
Provides Variation, Structural Variation phenotype association data
COSMIC 71 Somatic mutations found in human cancers from the COSMIC project (mapped to GRCh38)
Variation
2.1 million+
Link
Phenotype
2.2 million+
Link
Provides Variation phenotype association data
dbGaP 05/2014 The database of Genotypes and Phenotypes.
Phenotype
35,000+
Link
Study
Provides Variation phenotype association data
DDG2P 18/11/2014 Developmental Disorders Genotype-to-Phenotype Database
Phenotype
2,000+
Link
Provides Gene phenotype association data
DGVa 05/2015 Database of Genomic Variants Archive
SV
3.3 million+
Link
Phenotype
33,000+
Link
Study
Provides Structural Variation phenotype association data
EGA 05/2015 Variants imported from the European Genome-phenome Archive with phenotype association
Study
ESP 03/11/2014 Data from NHLBI ESP version v.0.0.30. 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
90,000+
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 Variation phenotype association 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 Variation phenotype association data
HGMD-PUBLIC 2014.4 Variants from HGMD-PUBLIC dataset December 2014 (mapped to GRCh38)
Variation
102,000+
Link
Phenotype
102,000+
Link
Provides Variation phenotype association data
IIBDGC 1 International Inflammatory Bowel Disease Genetics Consortium
Phenotype
10,000+
Link
Provides Variation phenotype association data
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 Variation phenotype association data
MIM disease 12/06/2015 Online Mendelian Inheritance in Man (OMIM) database
Phenotype
5,000+
Link
Provides Gene phenotype association data
NHGRI-EBI GWAS catalog 25/05/2015 Variants associated with phenotype data from the NHGRI-EBI GWAS catalog
Phenotype
22,000+
Link
Study
Provides Variation phenotype association data
OMIM 25/05/2015 Variations linked to entries in the Online Mendelian Inheritance in Man (OMIM) database
Phenotype
18,000+
Link
Study
Provides Variation phenotype association data
Orphanet 25/06/2014 The portal for rare diseases and drugs
Phenotype
5,000+
Link
Provides Gene phenotype association 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
881
Link
-
Teslovich 1 Biological, clinical and population relevance of 95 loci for blood lipids
Phenotype
7,000+
Link
Provides Variation phenotype association data
Uniprot 29/04/2015 Variants with protein annotation imported from Uniprot
Synonym
37,000+
Link
Phenotype
3,000+
Link
Study
Provides Variation phenotype association 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
24,000+
Link
Set
531,000+
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
1.1 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
931,000+
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
2.4 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
148
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
LSDB - Variants dbSNP annotates as being from LSDBs
Synonym
101,000+
Link
OIVD - Osteogenesis Imperfecta Variant Database
Synonym
777
Link
PAHdb - Phenylalanine hydroxylase database
Synonym
541
Link

Others species

Cat

Cat (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 30/03/2015 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
46
Link
Provides Gene phenotype association data
Chicken

Chicken (Gallus gallus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 140 Variants (including SNPs and indels) imported from dbSNP
Variation
9.5 million+
Link
Archive dbSNP 140 Former variants names imported from dbSNP
Synonym
27,000+
Link
Animal_QTLdb 27/04/2015 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 QTL phenotype association data
OMIA 30/03/2015 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 Gene phenotype association 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
Chimpanzee

Chimpanzee (Pan troglodytes)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP
Variation
1.6 million+
Link
OMIA 30/03/2015 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 Gene phenotype association data
Cow

Cow (Bos taurus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 143 Variants (including SNPs and indels) imported from dbSNP
Variation
95 million+
Link
Archive dbSNP 143 Former variants names imported from dbSNP
Synonym
524,000+
Link
Animal_QTLdb 27/04/2015 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
17,000+
Link
Study
Provides QTL phenotype association data
DGVa 05/2014 Database of Genomic Variants Archive
SV
2,000+
Link
Study
OMIA 27/04/2015 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
102
Link
Provides Gene phenotype association data
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Illumina BovineHD BeadChip - Variants from the Illumina BovineHD BeadChip genotyping array
Set
780,000+
Link
Illumina BovineLD BeadChip - Variants from the Illumina BovineLD BeadChip genotyping array
Set
7,000+
Link
Illumina BovineSNP50 BeadChip - Variants from the Illumina BovineSNP50 BeadChip genotyping array
Set
56,000+
Link
Dog

Dog (Canis familiaris)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
3.2 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
Study
OMIA 26/05/2015 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
159
Link
Provides Gene phenotype association data
Fruitfly

Fruitfly (Drosophila melanogaster)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
DPGP 1 Variation features from DPGP, with Ensembl identifiers
Variation
6.7 million+
Link
Gibbon

Gibbon (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
1.1 million+
Link
Horse

Horse (Equus caballus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
4.9 million+
Link
Archive dbSNP 139 Former variants names imported from dbSNP
Synonym
4,000+
Link
Animal_QTLdb 27/04/2015 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
1,000+
Link
Study
Provides QTL phenotype association data
DGVa 05/2014 Database of Genomic Variants Archive
SV
193,000+
Link
Study
OMIA 26/05/2015 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 Gene phenotype association 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
Macaque

Macaque (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 30/03/2015 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 Gene phenotype association data
Mouse

Mouse (Mus musculus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 142 Variants (including SNPs and indels) imported from dbSNP
Variation
80 million+
Link
Archive dbSNP 142 Former variants names imported from dbSNP
Synonym
255,000+
Link
3i 29/04/2015 Infection, Immunity and Immunophenotyping consortium
Phenotype
277
Link
Provides Gene phenotype association data
DGVa 05/2015 Database of Genomic Variants Archive
SV
791,000+
Link
Study
EuroPhenome 29/04/2015 EuroPhenome
Phenotype
2,000+
Link
Provides Gene phenotype association data
IMPC 29/04/2015 International Mouse Phenotyping Consortium
Phenotype
5,000+
Link
Provides Gene phenotype association data
MGP 29/04/2015 WTSI Mouse Genetics Project
Phenotype
1,000+
Link
Provides Gene phenotype association data
Opossum

Opossum (Monodelphis domestica)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
1.1 million+
Link
Orangutan

Orangutan (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
Pig

Pig (Sus scrofa)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 143 Variants (including SNPs and indels) imported from dbSNP
Variation
52 million+
Link
Archive dbSNP 143 Former variants names imported from dbSNP
Synonym
3,000+
Link
Animal_QTLdb 27/04/2015 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
12,000+
Link
Study
Provides QTL phenotype association data
DGVa 05/2014 Database of Genomic Variants Archive
SV
85
Link
Study
Pig SNP Consortium 0 PorcineSNP60 BeadChip
Variation
157
Link
Synonym
63,000+
Link
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Illumina_PorcineSNP60 - PorcineSNP60 BeadChip
Set
63,000+
Link
Platypus

Platypus (Ornithorhynchus anatinus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
1.3 million+
Link
Ensembl 1 Original names assigned prior to dbSNP submission
Synonym
773,000+
Link
Rat

Rat (Rattus norvegicus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 138 Variants (including SNPs and indels) imported from dbSNP (mapped to Rnor_6.0)
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
2.4 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 19/05/2015 QTLs from the Rat Genome Database (RGD)
Phenotype
32,000+
Link
Provides Gene, QTL phenotype association data
S. cerevisiae

S. cerevisiae (Saccharomyces cerevisiae)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
SGRP - Variation features from SGRP, with Ensembl identifiers
Variation
263,000+
Link
Sheep

Sheep (Ovis aries)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 143 Variants (including SNPs and indels) imported from dbSNP
Variation
51 million+
Link
Archive dbSNP 143 Former variants names imported from dbSNP
Synonym
566
Link
Animal_QTLdb 27/04/2015 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
791
Link
Study
Provides QTL phenotype association data
DGVa 05/2015 Database of Genomic Variants Archive
SV
2
Link
Study
OMIA 27/04/2015 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
36
Link
Provides Gene phenotype association data
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
IlluminaOvineHDSNP - Illumina Ovine Infinium HD SNP BeadChip
Synonym
604,000+
Link
Set
604,000+
Link
IlluminaOvineSNP50 - Illumina OvineSNP50 BeadChip
Variation
7,000+
Link
Set
54,000+
Link
Tetraodon

Tetraodon (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
Turkey

Turkey (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 30/03/2015 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 Gene phenotype association data
Zebra Finch

Zebra Finch (Taeniopygia guttata)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 139 Variants (including SNPs and indels) imported from dbSNP
Variation
1.7 million+
Link
Archive dbSNP 139 Former variants names imported from dbSNP
Synonym
1,000+
Link
Zebrafish

Zebrafish (Danio rerio)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 142 Variants (including SNPs and indels) imported from dbSNP (mapped to GRCz10)
Variation
17 million+
Link
Archive dbSNP 142 Former variants names imported from dbSNP
Synonym
33,000+
Link
DGVa 05/2015 Database of Genomic Variants Archive
SV
5,000+
Link
Study
OMIA 30/03/2015 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 Gene phenotype association data
ZFIN 30/03/2015 The zebrafish model organism database
Phenotype
34,000+
Link
Provides Gene phenotype association data