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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 - Human data sources

We provide data from a variety of sources. To view variants specific to these data sets in the browser go to a Location page 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.

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
9.1 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 11/2019 Catalog of genes of which mutations have been causally implicated in cancer
Phenotype
48 K
Link
Provides Gene phenotype association data
ClinVar 12/2019 Variants of clinical significance imported from ClinVar
Variant
1
Link
Synonym
1 M
Link
Phenotype
688 K
Link
Provides Variation phenotype association data
COSMIC 90 Somatic mutations found in human cancers from the COSMIC catalogue
Variant
9.5 M
Link
Synonym
3.1 M
Link
Phenotype
9.8 M
Link
Provides Variation phenotype association data
dbGaP 05/2014 The database of Genotypes and Phenotypes.
Phenotype
39 K
Link
Provides Variation phenotype association data
dbVar 01/2020 NCBI database of human genomic structural variation
SV
562 K
Link
Phenotype
584 K
Link
Provides Structural Variation phenotype association data
DDG2P 28/01/2020 Developmental Disorders Genotype-to-Phenotype Database
Phenotype
2 K
Link
Provides Gene phenotype association data
DGVa 01/2020 Database of Genomic Variants Archive
SV
4.8 M
Link
Phenotype
127 K
Link
Provides Structural Variation phenotype association data
EGA 12/2019 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
4 K
Link
Provides Variation phenotype association data
HGMD-PUBLIC 2019.4 Variants from HGMD-PUBLIC dataset December 2019
Variant
168 K
Link
Phenotype
168 K
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 K
Link
Provides Variation phenotype association data
MIM morbid 28/01/2020 Online Mendelian Inheritance in Man (OMIM) database
Phenotype
5 K
Link
Provides Gene phenotype association data
NHGRI-EBI GWAS catalog 16/12/2019 Variants associated with phenotype data from the NHGRI-EBI GWAS catalog
Phenotype
196 K
Link
Provides Variation phenotype association data
OMIM 12/2019 Variants linked to entries in the Online Mendelian Inheritance in Man (OMIM) database [imported via ClinVar]
Synonym
24 K
Link
Orphanet 01/01/2020 The portal for rare diseases and drugs
Phenotype
7 K
Link
Provides Gene phenotype association data
PharmGKB 17/02/2020 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
SV
3 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 17/02/2020 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
dbPEX - dbPEX, PEX Gene Database
Synonym
146
Link
HbVar - A Database of Human Hemoglobin Variants and Thalassemias
Synonym
1 K
Link
Infevers - The registry of Hereditary Auto-inflammatory Disorders Mutations
Synonym
617
Link
KAT6BDB - K(lysine) acetyltransferase 6B database, BCM
Synonym
19
Link
LMDD - Leiden Muscular Dystrophy Database
Synonym
677
Link
OIVD - Osteogenesis Imperfecta Variant Database
Synonym
770
Link
PAHdb - Phenylalanine hydroxylase database
Synonym
541
Link