Icons legend
| New version of the data source in this release for the species |
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| New data source in this release for the species |
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Source which provides phenotype association data |
| The source contains only germline data |
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| The source contains only somatic data |
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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 - 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 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 (Homo sapiens)
| Source | Version | Description | Data type(s)
Type
Count
e.g.
|
Other | ||
|---|---|---|---|---|---|---|
| dbSNP | 156 | Variants (including SNPs and indels) imported from dbSNP | Variant
1 B
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| Archive dbSNP | 156 | Former dbSNP variant names, merged by variant | Synonym
11 M
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| dbSNP HGVS | 156 | HGVS annotation from dbSNP | Synonym
275 M
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| Former dbSNP | 156 | Former dbSNP variant names, merged by allele | Synonym
572 K
|
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| 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
|
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| Cancer Gene Census | 06/2023 | Catalog of genes of which mutations have been causally implicated in cancer | Phenotype
43 K
|
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| ClinVar | 06/2023 | Variants of clinical significance imported from ClinVar | Variant
Synonym
4.5 M
Phenotype
2.6 M
|
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| COSMIC | 98 | Somatic mutations found in human cancers from the COSMIC catalogue | Variant
13 M
Synonym
5.2 M
Phenotype
13 M
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| dbGaP | 05/2014 | The database of Genotypes and Phenotypes. | Phenotype
39 K
|
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| dbVar | 08/2023 | NCBI database of human genomic structural variation | SV
1.7 M
Phenotype
738 K
|
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| DDG2P | 15/01/2021 | Developmental Disorders Genotype-to-Phenotype Database | Phenotype
2 K
|
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| DGVa | 01/2020 | Database of Genomic Variants Archive | SV
4.8 M
Phenotype
128 K
|
|
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| G2P | 21/06/2023 | Genotype-to-Phenotype Database | Phenotype
3 K
|
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| GEFOS | 1 | The GEnetic Factors for OSteoporosis Consortium international collaboration that seeks to identify common risk gene variants for osteoporosis | Phenotype
1 K
|
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| 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
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| HGMD-PUBLIC | 2020.4 | Variants from HGMD-PUBLIC dataset December 2020 | Variant
187 K
Phenotype
187 K
|
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| 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
|
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| MIM morbid | 21/06/2023 | Online Mendelian Inheritance in Man (OMIM) database | Phenotype
5 K
|
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| NHGRI-EBI GWAS catalog | 03/06/2023 | Variants associated with phenotype data from the NHGRI-EBI GWAS catalog | Phenotype
576 K
|
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| OMIM | 06/2023 | Variants linked to entries in the Online Mendelian Inheritance in Man (OMIM) database [imported via ClinVar] | Synonym
30 K
|
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| Orphanet | 28/11/2022 | The portal for rare diseases and drugs | Phenotype
8 K
|
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| PharmGKB | 13/06/2023 | A pharmacogenomics knowledge resource | Synonym
7 K
|
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| PhenCode | - | PhenCode is a collaborative project to better understand the relationship between genotype and phenotype in humans | SV
3 K
|
- | ||
| Teslovich | 1 | Biological, clinical and population relevance of 95 loci for blood lipids | Phenotype
7 K
|
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| UniProt | 13/06/2023 | Variants with protein annotation imported from UniProt | Synonym
64 K
|
|
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| Chip Source | Version | Description | 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
|
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| 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
|
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| 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
588 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
|
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| Affy GeneChip 500K | - | Variants from the Affymetrix GeneChip Human Mapping 500K Array Set |
Set
494 K
|
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| 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
|
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| Illumina_HumanOmni1-Quad | - | Variants from the Illumina HumanOmni1-Quad whole genome genotyping array designed for association studies |
Set
1 M
|
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| 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
|
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| LSDB Source | Version | Description | Data type(s)
Type
Count
e.g.
|
Other | ||
|---|---|---|---|---|---|---|
| dbPEX | - | dbPEX, PEX Gene Database | Synonym
145
|
|||
| HbVar | - | A Database of Human Hemoglobin Variants and Thalassemias | Synonym
1 K
|
|||
| Infevers | - | The registry of Hereditary Auto-inflammatory Disorders Mutations | Synonym
616
|
|||
| KAT6BDB | - | K(lysine) acetyltransferase 6B database, BCM | Synonym
19
|
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| LMDD | - | Leiden Muscular Dystrophy Database | Synonym
677
|
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| OIVD | - | Osteogenesis Imperfecta Variant Database | Synonym
771
|
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| PAHdb | - | Phenylalanine hydroxylase database | Synonym
540
|
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