In the first quarter of 2020 we will be removing all data other than for human from this archive website. Please read our blog post for full details.

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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 - entries count:
greater than 100 million
from 10 to 99.9 million
from 1 million to 9.9 million
from 1,000 to 999,999
less than 1,000

Ensembl Variation - Data sources

List of data sources for each species - Ensembl 99

We provide data from a variety of sources. To view variants specific to these data sets in the browser go to a species Location page (e.g. for human), and click on the 'Configure this page' link on the left-hand side. The 'Variation' and 'Somatic mutations' sections contain a track list of all the sources of variant data for that species.

Human

Human (Homo sapiens)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 153 Variants (including SNPs and indels) imported from dbSNP
Variant
667 M
Link
Archive dbSNP 153 Former dbSNP variant names, merged by variant
Synonym
11 M
Link
dbSNP HGVS 153 HGVS annotation from dbSNP
Synonym
128 M
Link
Former dbSNP 153 Former dbSNP variant names, merged by allele
Synonym
10 M
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 K
Link
Provides Variation phenotype association data
Cancer Gene Census 09/2019 Catalog of genes of which mutations have been causally implicated in cancer
Phenotype
30 K
Link
Provides Gene phenotype association data
ClinVar 09/2019 Variants of clinical significance imported from ClinVar
Variant
3
Link
Synonym
651 K
Link
Phenotype
686 K
Link
Provides Variation phenotype association data
COSMIC 90 Somatic mutations found in human cancers from the COSMIC catalogue
Variant
10 M
Link
Synonym
3.3 M
Link
Phenotype
10 M
Link
Provides Variation phenotype association data
dbGaP 05/2014 The database of Genotypes and Phenotypes.
Phenotype
40 K
Link
Provides Variation phenotype association data
dbPEX - dbPEX, PEX Gene Database
Synonym
146
Link
dbVar 10/2019 NCBI database of human genomic structural variation
SV
60 K
Link
Phenotype
83 K
Link
Provides Structural Variation phenotype association data
DDG2P 10/10/2019 Developmental Disorders Genotype-to-Phenotype Database
Phenotype
2 K
Link
Provides Gene phenotype association data
DGVa 01/2019 Database of Genomic Variants Archive
SV
4.9 M
Link
Phenotype
48 K
Link
Provides Structural Variation phenotype association data
EGA 10/2019 Variants imported from the European Genome-phenome Archive with phenotype association
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.
Variant
GEFOS 1 The GEnetic Factors for OSteoporosis Consortium international collaboration that seeks to identify common risk gene variants for osteoporosis
Phenotype
1 K
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 K
Link
Provides Variation phenotype association data
HGMD-PUBLIC 2018.4 Variants from HGMD-PUBLIC dataset December 2018
Variant
152 K
Link
Phenotype
152 K
Link
Provides Variation phenotype association data
Infevers - The registry of Hereditary Auto-inflammatory Disorders Mutations
Synonym
617
Link
KAT6BDB - K(lysine) acetyltransferase 6B database, BCM
Synonym
19
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 K
Link
Provides Variation phenotype association data
MIM morbid 10/10/2019 Online Mendelian Inheritance in Man (OMIM) database
Phenotype
8 K
Link
Provides Gene phenotype association data
NHGRI-EBI GWAS catalog 24/09/2019 Variants associated with phenotype data from the NHGRI-EBI GWAS catalog
Phenotype
190 K
Link
Provides Variation phenotype association data
OIVD - Osteogenesis Imperfecta Variant Database
Synonym
770
Link
OMIM 09/2019 Variants linked to entries in the Online Mendelian Inheritance in Man (OMIM) database [imported via ClinVar]
Synonym
24 K
Link
Orphanet 01/10/2019 The portal for rare diseases and drugs
Phenotype
7 K
Link
Provides Gene phenotype association data
PAHdb - Phenylalanine hydroxylase database
Synonym
541
Link
PharmGKB 22/10/2019 A pharmacogenomics knowledge resource
Synonym
6 K
Link
PhenCode - PhenCode is a collaborative project to better understand the relationship between genotype and phenotype in humans
Synonym
11 K
Link
Teslovich 1 Biological, clinical and population relevance of 95 loci for blood lipids
Phenotype
7 K
Link
Provides Variation phenotype association data
Uniprot 23/10/2019 Variants with protein annotation imported from Uniprot
Synonym
61 K
Link
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 K
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 K
Link
Illumina_Human1M-duo 3 Variants from the Illumina Human 1M-Duo v3 whole genome SNP genotyping chip designed for association studies
SV
35 K
Link
Illumina_Human660W-quad - Variants from the Illumina Human 660W-Quad whole genome SNP genotyping chip designed for association studies
SV
64 K
Link
Set
589 K
Link
Affy GenomeWideSNP_6.0 - Variants from the Affymetrix Genome-Wide Human SNP Array 6.0
Set
928 K
Link
Illumina_1M-duo - Variants from the Illumina Human1M-duo v3 whole genome genotyping array designed for association studies
Set
1.1 M
Link
Affy GeneChip 500K - Variants from the Affymetrix GeneChip Human Mapping 500K Array Set
Set
494 K
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 K
Link
Illumina_HumanOmni1-Quad - Variants from the Illumina HumanOmni1-Quad whole genome genotyping array designed for association studies
Set
1 M
Link
Illumina_HumanHap650Y - Variants from the Illumina HumanHap650Y v3.0 whole genome genotyping array designed for association studies
Set
659 K
Link
Illumina_HumanOmni2.5 - Variants from the Illumina HumanOmni2.5 4v1 whole genome genotyping array designed for association studies
Set
2.4 M
Link
Illumina_Human610_Quad - Variants from the Illumina Human610_Quad v1_B whole genome genotyping array designed for association studies
Set
596 K
Link
Illumina_HumanHap550 - Variants from the Illumina Human550 v3.0 whole genome genotyping array designed for association studies
Set
560 K
Link
Illumina_HumanOmni5 - Variants from the Illumina HumanOmni5v1 whole genome genotyping array designed for association studies
Set
4 M
Link
Illumina_ExomeChip - Variants from the Illumina ExomeChip genotyping array designed to target variants within exons
Set
296 K
Link
Illumina_ImmunoChip - Variants from the Illumina ImmunoChip genotyping array designed to target variants of interest for autoimmune and inflammatory diseases
Set
187 K
Link
HumanOmniExpress - Variants from the Illumina HumanOmniExpress 12v1-1_a whole genome genotyping array
Set
718 K
Link
HumanCoreExome-12 - Variants from the Illumina HumanCoreExome-12 v1 genotyping chip.
Set
528 K
Link
LSDB SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
HbVar - A Database of Human Hemoglobin Variants and Thalassemias
Synonym
1 K
Link
LMDD - Leiden Muscular Dystrophy Database
Synonym
677
Link

Other species

Atlantic salmon

Atlantic salmon (Salmo salar)

New species!
SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
PRJEB34225 - Whole genome variants for 80 North American Atlantic salmon individuals
Variant (from VCF)
Cat

Cat (Felis catus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 148 Variants (including SNPs and indels) imported from dbSNP (mapped to Felis_catus_9.0)
Variant
3.6 M
Link
Archive dbSNP 148 Former variants names imported from dbSNP
Synonym
1 K
Link
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
59
Link
Provides Gene phenotype association data
Chicken

Chicken (Gallus gallus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 150 Variants (including SNPs and indels) imported from dbSNP [remapped to GRCg6a]
Variant
24 M
Link
Archive dbSNP 150 Former variants names imported from dbSNP
Synonym
34 K
Link
Animal_QTLdb 22/08/2018 The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and association data on livestock animal species [remapped to GRCg6a]
Phenotype
5 K
Link
Provides QTL phenotype association data
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
44
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 K
Link
Chimpanzee

Chimpanzee (Pan troglodytes)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP
Variant
1.6 M
Link
Cow

Cow (Bos taurus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 150 Variants (including SNPs and indels) imported from dbSNP [remapped to ARS-UCD1.2]
Variant
104 M
Link
Archive dbSNP 150 Former variants names imported from dbSNP
Synonym
570 K
Link
Animal_QTLdb 23/08/2019 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
97 K
Provides QTL phenotype association data
DGVa 07/2018 Database of Genomic Variants Archive [remapped to ARS-UCD1.2]
SV
18 K
Link
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
145
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 K
Link
Illumina BovineLD BeadChip - Variants from the Illumina BovineLD BeadChip genotyping array
Set
7 K
Link
Illumina BovineSNP50 BeadChip - Variants from the Illumina BovineSNP50 BeadChip genotyping array
Set
56 K
Link
Dog

Dog (Canis familiaris)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 151 Variants (including SNPs and indels) imported from dbSNP
Variant
5.9 M
Link
Archive dbSNP 151 Former variants names imported from dbSNP
Synonym
69 K
Link
DGVa 06/2017 Database of Genomic Variants Archive
SV
104 K
Link
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
247
Link
Provides Gene phenotype association data
Gibbon

Gibbon (Nomascus leucogenys)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 145 Variants (including SNPs and indels) imported from dbSNP [mapped to the assembly Nleu1.0]
Variant
1.1 M
Link
ENSEMBL - Variants for northern white-cheeked gibbon genome of a wild-born female named 'Asia' called by ENSEMBL pipeline
Synonym
1.1 M
Link
Goat

Goat (Capra hircus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 143 Variants (including SNPs and indels) imported from dbSNP
Variant
37 M
Link
Synonym
55 M
Link
Archive dbSNP 143 Former variants names imported from dbSNP
Synonym
1
Link
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
8
Link
Provides Gene phenotype association data
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Illumina_GoatSNP50 - Variants from the Illumina GoatSNP50 genotyping array
Set
59 K
Link
Horse

Horse (Equus caballus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 151 Variants (including SNPs and indels) imported from dbSNP [remapped to EquCab3.0]
Variant
21 M
Link
Archive dbSNP 151 Former variants names imported from dbSNP
Synonym
4 K
Link
Animal_QTLdb 26/08/2017 The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house all publicly available QTL and association data on livestock animal species [remapped to EquCab3.0]
Phenotype
808
Link
Provides QTL phenotype association data
DGVa 03/2017 Database of Genomic Variants Archive [remapped to EquCab3.0]
SV
193 K
Link
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
44
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 K
Link
Macaque

Macaque (Macaca mulatta)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 150 Variants (including SNPs and indels) imported from dbSNP [remapped to Mmul_10]
Variant
53 M
Link
Archive dbSNP 150 Former variants names imported from dbSNP
Synonym
9 K
Link
DGVa 10/2016 Database of Genomic Variants Archive
SV
110
Link
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
7
Link
Provides Gene phenotype association data
Mouse

Mouse (Mus musculus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 150 Variants (including SNPs and indels) imported from dbSNP
Variant
84 M
Link
Archive dbSNP 150 Former variants names imported from dbSNP
Synonym
294 K
Link
DGVa 05/2018 Database of Genomic Variants Archive
SV
791 K
Link
IMPC 26/06/2019 International Mouse Phenotyping Consortium
Phenotype
19 K
Link
Provides Gene phenotype association data
MGI 26/06/2019 Mouse Genome Informatics
Phenotype
150 K
Link
Provides Gene phenotype association data
Opossum

Opossum (Monodelphis domestica)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 149 Variants (including SNPs and indels) imported from dbSNP [remapped to ASM229v1]
Variant
1.1 M
Link
Archive dbSNP 149 Former variants names imported from dbSNP
Synonym
4 K
Link
Orangutan

Orangutan (Pongo abelii)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 136 Variants (including SNPs and indels) imported from dbSNP
Variant
10 M
Link
Pig

Pig (Sus scrofa)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 150 Variants (including SNPs and indels) imported from dbSNP
Variant
67 M
Link
Archive dbSNP 150 Former variants names imported from dbSNP
Synonym
24 K
Link
Animal_QTLdb 23/08/2019 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
19 K
Provides QTL phenotype association data
DGVa 03/2017 Database of Genomic Variants Archive
SV
224 K
Link
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
32
Link
Provides Gene phenotype association data
Pig SNP Consortium 0 PorcineSNP60 BeadChip
Variant
145
Link
Synonym
63 K
Link
Chip SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
Axiom Genotyping Array 1 Axiom Porcine Genotyping Array from Affymetrix
Variant
18 K
Link
Synonym
640 K
Link
Set
658 K
Link
GGP Porcine HD 15/05/2013 GeneSeek Genomic Profiler Porcine - HD
Synonym
68 K
Link
GGP Porcine LD 13/07/2012 GeneSeek Genomic Profiler Porcine - LD BeadChip
Synonym
9 K
Link
Illumina_PorcineSNP60 - PorcineSNP60 BeadChip
Set
63 K
Link
Platypus

Platypus (Ornithorhynchus anatinus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 149 Variants (including SNPs and indels) imported from dbSNP
Variant
1.3 M
Link
Archive dbSNP 149 Former variants names imported from dbSNP
Synonym
3 K
Link
Rat

Rat (Rattus norvegicus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 149 Variants (including SNPs and indels) imported from dbSNP
Variant
5 M
Link
Archive dbSNP 149 Former variants names imported from dbSNP
Synonym
180 K
Link
ENSEMBL:celera - Variants from Celera called by the ENSEMBL pipeline
Synonym
2.4 M
Link
ENSEMBL:RNB1 - Variants in RNB1 called by the ENSEMBL pipeline
Synonym
83 K
Link
ENSEMBL:STAR-4strain - Variants in STAR-4strain called by the ENSEMBL pipeline
Synonym
125 K
Link
ENSEMBL:STAR-gtype - Variants in STAR-gtype called by the ENSEMBL pipeline
Synonym
20 K
Link
RGD 18/10/2019 QTLs from the Rat Genome Database (RGD)
Phenotype
87 K
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
Variant
263 K
Link
Sheep

Sheep (Ovis aries)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 150 Variants (including SNPs and indels) imported from dbSNP
Variant
61 M
Link
Archive dbSNP 150 Former variants names imported from dbSNP
Synonym
775
Link
Animal_QTLdb 23/08/2019 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
2 K
Provides QTL phenotype association data
DGVa 05/2018 Database of Genomic Variants Archive
SV
2
Link
OMIA 24/10/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
50
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 K
Link
Set
604 K
Link
IlluminaOvineSNP50 - Illumina OvineSNP50 BeadChip
Set
48 K
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
Variant
902 K
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
Variant
9 K
Link
GOA 18/10/2016 Inferred from Mutant Phenotype (IMP), annotated by Gene Ontology Annotation
Phenotype
39
Link
Provides Gene phenotype association data
OMIA 18/07/2019 Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 200 animal species (other than human and mouse)
Phenotype
3
Link
Provides Gene phenotype association data
Vervet-AGM

Vervet-AGM (Chlorocebus sabaeus)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
PRJEB22989 - Effect annotated whole genome variants for 163 vervet monkeys (SNPs, Indels, and macaque fixed differences)
Variant (from VCF)
Zebra finch

Zebra finch (Taeniopygia guttata)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 148 Variants (including SNPs and indels) imported from dbSNP [remapped to bTaeGut1_v1]
Variant
1.7 M
Link
Archive dbSNP 148 Former variants names imported from dbSNP
Synonym
1 K
Link
Zebrafish

Zebrafish (Danio rerio)

SourceVersionDescription Data type(s)
Type
Count
e.g.
Other
dbSNP 150 Variants (including SNPs and indels) imported from dbSNP (mapped to GRCz11)
Variant
17 M
Link
Archive dbSNP 150 Former variants names imported from dbSNP
Synonym
33 K
Link
DGVa 07/2015 Database of Genomic Variants Archive
SV
5 K
Link
ZFIN 23/10/2019 The zebrafish model organism database
Phenotype
66 K
Link
Provides Gene phenotype association data