Species list

Human

American bison

American mink

Atlantic salmon

Cat

Chicken

Chicken (Red Jungle fowl)

Chimpanzee

Collared flycatcher

Cow

Crab-eating macaque

Dog

Dog - Boxer

Domestic yak

European seabass

Gibbon

Goat

Great Tit

Greater amberjack

Guinea Pig

Horse

Japanese quail

Macaque

Mallard

Mouse

Nile tilapia

Opossum

Pig

Pike-perch

Platypus

Prairie vole

Rabbit

Rainbow trout

Rat

Sheep

Sheep - Texel

Sumatran orangutan

Tetraodon

Turkey

Vervet-AGM

White-tufted-ear marmoset

Zebra finch

Zebrafish

# : New data version(s)

# : New data source(s)

Icons legend

[Top]

	New version of the data source in this release for the species
	New data source in this release for the species
	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 1 billion
	from 100 million to 999.9 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 113

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.

See documentation for the detailed phenotype/disease/trait association sources →

Human (Homo sapiens)

	Version	Description	Data type(s) Type Count e.g.
dbSNP	156	Variants (including SNPs and indels) imported from dbSNP	Variant 1 B
Archive dbSNP	156	Former dbSNP variant names, merged by variant	Synonym 20 M
dbSNP HGVS	156	HGVS annotation from dbSNP	Synonym 273 M
Former dbSNP	156	Former dbSNP variant names, merged by allele	Synonym 576 K
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
Cancer Gene Census	06/2024	Catalog of genes of which mutations have been causally implicated in cancer	Phenotype 66 K
ClinVar	04/2024	Variants of clinical significance imported from ClinVar	Variant 93 Synonym 5.5 M Phenotype 3.3 M
COSMIC	99	Somatic mutations found in human cancers from the COSMIC catalogue	Variant 13 M Synonym 5.4 M Phenotype 14 M
dbGaP	05/2014	The database of Genotypes and Phenotypes.	Phenotype 40 K
dbPEX	-	dbPEX, PEX Gene Database	Synonym 146
dbVar	10/2023	NCBI database of human genomic structural variation	SV 1.7 M Phenotype 109 K
DGVa	01/2020	Database of Genomic Variants Archive	SV 5 M Phenotype 122 K
G2P	20/06/2024	Genotype-to-Phenotype Database	Phenotype 4 K
GEFOS	1	The GEnetic Factors for OSteoporosis Consortium international collaboration that seeks to identify common risk gene variants for osteoporosis	Phenotype 1 K
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
HGMD-PUBLIC	2020.4	Variants from HGMD-PUBLIC dataset December 2020	Variant 187 K Phenotype 187 K
Infevers	-	The registry of Hereditary Auto-inflammatory Disorders Mutations	Synonym 617
KAT6BDB	-	K(lysine) acetyltransferase 6B database, BCM	Synonym 19
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
MIM morbid	20/06/2024	Online Mendelian Inheritance in Man (OMIM) database	Phenotype 10 K
NHGRI-EBI GWAS catalog	20/05/2024	Variants associated with phenotype data from the NHGRI-EBI GWAS catalog	Phenotype 698 K
OIVD	-	Osteogenesis Imperfecta Variant Database	Synonym 771
OMIM	04/2024	Variants linked to entries in the Online Mendelian Inheritance in Man (OMIM) database [imported via ClinVar]	Synonym 31 K
Orphanet	04/12/2023	The portal for rare diseases and drugs	Phenotype 8 K
PAHdb	-	Phenylalanine hydroxylase database	Synonym 547
PharmGKB	21/05/2024	A pharmacogenomics knowledge resource	Synonym 8 K
PhenCode	-	PhenCode is a collaborative project to better understand the relationship between genotype and phenotype in humans	Synonym 11 K
Teslovich	1	Biological, clinical and population relevance of 95 loci for blood lipids	Phenotype 7 K
UniProt	21/05/2024	Variants with protein annotation imported from UniProt	Synonym 65 K

	Version	Description	Data type(s) Type Count e.g.
Affy GenomeWideSNP_6 CNV	-	Copy Number Variation (CNV) probes from the Affymetrix Genome-Wide Human SNP Array 6.0	SV 945 K
Illumina_CytoSNP12v1	1	Variants from the Illumina Cyto SNP-12 v1 whole genome SNP genotyping chip designed for cytogenetic analysis	SV 496 Set 51 K
Illumina_Human1M-duo	3	Variants from the Illumina Human 1M-Duo v3 whole genome SNP genotyping chip designed for association studies	SV 35 K
Illumina_Human660W-quad	-	Variants from the Illumina Human 660W-Quad whole genome SNP genotyping chip designed for association studies	SV 64 K Set 589 K
Affy GenomeWideSNP_6.0	-	Variants from the Affymetrix Genome-Wide Human SNP Array 6.0	Set 928 K
Illumina_1M-duo	-	Variants from the Illumina Human1M-duo v3 whole genome genotyping array designed for association studies	Set 1.1 M
Affy GeneChip 500K	-	Variants from the Affymetrix GeneChip Human Mapping 500K Array Set	Set 494 K
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
Illumina_HumanOmni1-Quad	-	Variants from the Illumina HumanOmni1-Quad whole genome genotyping array designed for association studies	Set 1 M
Illumina_HumanHap650Y	-	Variants from the Illumina HumanHap650Y v3.0 whole genome genotyping array designed for association studies	Set 659 K
Illumina_HumanOmni2.5	-	Variants from the Illumina HumanOmni2.5 4v1 whole genome genotyping array designed for association studies	Set 2.4 M
Illumina_Human610_Quad	-	Variants from the Illumina Human610_Quad v1_B whole genome genotyping array designed for association studies	Set 596 K
Illumina_HumanHap550	-	Variants from the Illumina Human550 v3.0 whole genome genotyping array designed for association studies	Set 560 K
Illumina_HumanOmni5	-	Variants from the Illumina HumanOmni5v1 whole genome genotyping array designed for association studies	Set 4 M
Illumina_ExomeChip	-	Variants from the Illumina ExomeChip genotyping array designed to target variants within exons	Set 296 K
Illumina_ImmunoChip	-	Variants from the Illumina ImmunoChip genotyping array designed to target variants of interest for autoimmune and inflammatory diseases	Set 187 K
HumanOmniExpress	-	Variants from the Illumina HumanOmniExpress 12v1-1_a whole genome genotyping array	Set 718 K
HumanCoreExome-12	-	Variants from the Illumina HumanCoreExome-12 v1 genotyping chip.	Set 528 K

LSDB Source		Version	Description	Data type(s) Type Count e.g.	Other
	HbVar	-	A Database of Human Hemoglobin Variants and Thalassemias	Synonym 1 K
	LMDD	-	Leiden Muscular Dystrophy Database	Synonym 678

Other species

American bison (Bison bison bison)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 19 K

American mink (Neovison vison)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	PRJEB26368			Variant (from VCF) 34 K
	EVA	5	Variants imported from EVA	Variant (from VCF) 34 K

Atlantic salmon (Salmo salar)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	PRJEB34225	-	Variants with genotypes imported from EVA	Variant (from VCF) 8 M
	EVA	5	Variants imported from EVA	Variant (from VCF) 15 M

Cat (Felis catus)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	4	Short variant data imported from EVA	Variant 3.2 M
	OMIA	19/06/2024	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 106

Chicken (Gallus gallus)

	Version	Description	Data type(s) Type Count e.g.
Animal_QTLdb	27/04/2024	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 14 K
EVA	4	Short variant data imported from EVA	Variant 25 M
OMIA	19/06/2024	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 56

Chip Source		Version	Description	Data type(s) Type Count e.g.	Other
	Affymetrix Chicken600K Array	-	Variants from the Affymetrix Chicken600K genotyping array	Set 571 K

Chicken (Red Jungle fowl) (Gallus gallus gca000002315v5)

	Version	Description	Data type(s) Type Count e.g.
Animal_QTLdb	17/10/2022	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 K
EVA	4	Short variant data imported from EVA	Variant 27 M
OMIA	18/10/2022	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 54

Chip Source		Version	Description	Data type(s) Type Count e.g.	Other
	Affymetrix Chicken600K Array	-	Variants from the Affymetrix Chicken600K genotyping array	Set 572 K

Chimpanzee (Pan troglodytes)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 22 M

Collared flycatcher (Ficedula albicollis)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 37 K

Cow (Bos taurus)

	Version	Description	Data type(s) Type Count e.g.
Animal_QTLdb	27/04/2024	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 163 K
DGVa	07/2018	Database of Genomic Variants Archive [remapped to ARS-UCD1.3]	SV 18 K
EVA	4	Short variant data imported from EVA [remapped to ARS-UCD1.3]	Variant 96 M
OMIA	19/06/2024	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 198

	Version	Description	Data type(s) Type Count e.g.
Illumina BovineHD BeadChip	-	Variants from the Illumina BovineHD BeadChip genotyping array	Set 708 K
Illumina BovineLD BeadChip	-	Variants from the Illumina BovineLD BeadChip genotyping array	Set 6 K
Illumina BovineSNP50 BeadChip	-	Variants from the Illumina BovineSNP50 BeadChip genotyping array	Set 50 K

Crab-eating macaque (Macaca fascicularis)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 1.6 M

Dog (Canis lupus familiaris)

	Version	Description	Data type(s) Type Count e.g.
DGVa	06/2017	Database of Genomic Variants Archive [Remapped to ROS_Cfam_1.0]	SV 104 K
EVA	5	Short variant data imported from EVA	Variant 37 M
OMIA	19/06/2024	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 348

Dog - Boxer (Canis lupus familiarisboxer)

	Version	Description	Data type(s) Type Count e.g.
DGVa	06/2017	Database of Genomic Variants Archive [Remapped to ROS_Cfam_1.0]	SV 104 K
EVA	5	Short variant data imported from EVA	Variant 35 M
OMIA	19/06/2024	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 348

Domestic yak (Bos grunniens)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 64 K

European seabass (Dicentrarchus labrax)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 37 K

Gibbon (Nomascus leucogenys)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 1.1 M

Goat (Capra hircus)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	Animal_QTLdb	04/05/2024	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 K
	OMIA	19/06/2024	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 15

Chip Source		Version	Description	Data type(s) Type Count e.g.	Other
	Illumina_GoatSNP50	-	Variants from the Illumina GoatSNP50 genotyping array	Set 57 K

Great Tit (Parus major)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 498 K
	PRJEB24964	-	Variants with genotypes imported from EVA	Variant (from VCF) 497 K

Greater amberjack (Seriola dumerili)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 9 M

Guinea Pig (Cavia porcellus)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 844 K

Horse (Equus caballus)

	Version	Description	Data type(s) Type Count e.g.
Animal_QTLdb	27/04/2024	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
DGVa	03/2017	Database of Genomic Variants Archive [remapped to EquCab3.0]	SV 193 K
EVA	4	Short variant data imported from EVA	Variant 40 M
OMIA	19/06/2024	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

Chip Source		Version	Description	Data type(s) Type Count e.g.	Other
	Illumina EquineSNP50 BeadChip	-	Variants from the Illumina EquineSNP50 BeadChip genotyping array	Set 53 K

Japanese quail (Coturnix japonica)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 8 K

Macaque (Macaca mulatta)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 50 M

Mallard (Anas platyrhynchos)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 29 M

Mouse (Mus musculus)

	Version	Description	Data type(s) Type Count e.g.
DGVa	05/2018	Database of Genomic Variants Archive [remapped to GRCm39]	SV 791 K
EVA	4	Short variant data imported from EVA	Variant 122 M
IMPC	07/05/2024	International Mouse Phenotyping Consortium	Phenotype 43 K
MGI	07/05/2024	Mouse Genome Informatics	Phenotype 206 K

Nile tilapia (Oreochromis niloticus)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 18 M
	PRJEB38548			Variant (from VCF) 63 K

Opossum (Monodelphis domestica)

Source		Version	Description	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
	Archive dbSNP	149	Former variants names imported from dbSNP	Synonym 4 K

Pig (Sus scrofa)

	Version	Description	Data type(s) Type Count e.g.
Animal_QTLdb	27/04/2024	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 43 K
DGVa	03/2017	Database of Genomic Variants Archive	SV 224 K
EVA	4	Short variant data imported from EVA	Variant 71 M
OMIA	19/06/2024	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 72
Pig SNP Consortium	01/03/2023	PorcineSNP60 BeadChip	Variant Synonym 52 K

Chip Source		Version	Description	Data type(s) Type Count e.g.	Other
	Axiom Genotyping Array	1	Axiom Porcine Genotyping Array from Affymetrix	Variant Synonym Set 620 K
	Illumina_PorcineSNP60	-	PorcineSNP60 BeadChip	Set 57 K

Pike-perch (Sander lucioperca)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 975 K

Platypus (Ornithorhynchus anatinus)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	dbSNP	149	Variants (including SNPs and indels) imported from dbSNP [remapped to mOrnAna1.p.v1]	Variant 1.3 M
	Archive dbSNP	149	Former variants names imported from dbSNP	Synonym 3 K

Prairie vole (Microtus ochrogaster)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 8 K

Rabbit (Oryctolagus cuniculus)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	PRJEB27278	-	Variants with genotypes imported from EVA	Variant (from VCF) 82 K
	EVA	5	Variants imported from EVA	Variant (from VCF) 83 K

Rainbow trout (Oncorhynchus mykiss)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 33 K

Rat (Rattus norvegicus)

	Version	Description	Data type(s) Type Count e.g.
ENSEMBL:celera	-	Variants from Celera called by the ENSEMBL pipeline	Synonym 2.4 M
ENSEMBL:RNB1	-	Variants in RNB1 called by the ENSEMBL pipeline	Synonym 83 K
ENSEMBL:STAR-4strain	-	Variants in STAR-4strain called by the ENSEMBL pipeline	Synonym 125 K
ENSEMBL:STAR-gtype	-	Variants in STAR-gtype called by the ENSEMBL pipeline	Synonym 20 K
EVA	4	Short variant data imported from EVA	Variant 9.5 M
RGD	07/06/2024	QTLs from the Rat Genome Database (RGD)	Phenotype 134 K

Sheep (Ovis aries rambouillet)

	Version	Description	Data type(s) Type Count e.g.
Animal_QTLdb	27/04/2024	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 3 K
DGVa	05/2018	Database of Genomic Variants Archive [remapped to ARS-UI_Ramb_v2.0]	SV 2
EVA	5	Short variant data imported from EVA	Variant 89 M
OMIA	19/06/2024	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 55

Chip Source		Version	Description	Data type(s) Type Count e.g.	Other
	IlluminaOvineHDSNP	-	Illumina Ovine Infinium HD SNP BeadChip [remapped to ARS-UI_Ramb_v2.0]	Synonym Set 596 K
	IlluminaOvineSNP50	-	Illumina OvineSNP50 BeadChip	Set 47 K

Sheep - Texel (Ovis aries)

	Version	Description	Data type(s) Type Count e.g.
dbSNP	150	Variants (including SNPs and indels) imported from dbSNP	Variant 61 M
Archive dbSNP	150	Former variants names imported from dbSNP	Synonym 775
Animal_QTLdb	27/04/2024	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 144
DGVa	05/2018	Database of Genomic Variants Archive	SV 2
OMIA	19/06/2024	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 54

Chip Source		Version	Description	Data type(s) Type Count e.g.	Other
	IlluminaOvineHDSNP	-	Illumina Ovine Infinium HD SNP BeadChip	Synonym 604 K Set 604 K
	IlluminaOvineSNP50	-	Illumina OvineSNP50 BeadChip	Set 48 K

Sumatran orangutan (Pongo abelii)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 9.5 M

Tetraodon (Tetraodon nigroviridis)

Source		Version	Description	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
	Archive dbSNP	132	Former variants names imported from dbSNP	Synonym 956

Turkey (Meleagris gallopavo)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 5 K

Vervet-AGM (Chlorocebus sabaeus)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	PRJEB22989	-	Variants with genotypes imported from EVA	Variant (from VCF) 62 M
	EVA	5	Variants imported from EVA	Variant (from VCF) 67 M

White-tufted-ear marmoset (Callithrix jacchus)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 14 M

Zebra finch (Taeniopygia guttata)

Source		Version	Description	Data type(s) Type Count e.g.	Other
	EVA	5	Variants imported from EVA	Variant (from VCF) 1.5 M

Zebrafish (Danio rerio)

	Version	Description	Data type(s) Type Count e.g.
DGVa	07/2015	Database of Genomic Variants Archive	SV 5 K
EVA	4	Short variant data imported from EVA	Variant 18 M
ZFIN	18/06/2024	The zebrafish model organism database	Phenotype 88 K