Ensembl Variation - Data description
Below is a description of the data we store in the databases for Ensembl Variation. For several different species in Ensembl,
we import variation data (SNPs, CNVs, allele frequencies, genotypes etc) from a variety of
sources (e.g. dbSNP).
We classify the variants into different
classes and calculate the predicted consequence(s) of the variant. In human, we calculate the linkage disequilibrium for each variant, by population.
We have also created sets to help people retrieve a specific group of variants from a particular dataset.
Variation species and data sources
Ensembl stores variation data for the following species, but note that users can still use the Variant Effect Predictor on species for which we do not currently have a variation database.
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The majority of variants are imported from NCBI dbSNP. The data is imported when it is released by dbSNP and incorporated into the next Ensembl release. If dbSNP releases the data on a different assembly, Ensembl will remap the variant positions onto the current assembly. Data from projects like the HapMap Project and 1000 Genomes Project is imported once it has been submitted to dbSNP.
Ensembl also includes data from other sources. To view data from these sources 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 'Germline variation' and 'Somatic mutations' sections contain a track list of all sources of variation data for that species.
Variation displays
Variation data can be viewed in the browser through pages such as:
- Gene: Variation Table and Variation Image (for all variations in a gene) e.g. for example for all variants in KCNE2. Structural Variation to see all structural variants overlapping the gene.
- Transcript: Population comparison, Comparison image (for comparing variants in a transcript across different individual or strain sequences) e.g. compare Tmco4 in different mouse strains
- Transcript: Sequence, protein: list of the coding variants in protein coordinates.
- Location: Region in Detail (Variations can be drawn using "Configure this page" at the left. The menu allows display of information in Ensembl databases along with external sources in DAS format such as DGV loci.)
Clicking on any variation on an Ensembl page will open a Variation tab with information about the flanking sequence and source for the selected variation. Links to linkage disequilibrium (LD) plots, phenotype information (for human) from EGA, OMIM and NHGRI and Ensembl genes and transcripts that include the variation can be found at the left of this tab. You may also view multiple genome alignments of various species, highlighting the variation. Ancestral sequences are included in this display.
Variation information can also be accessed using BioMart (gene or variation database), and the Perl API (variation API).
Data types
The Ensembl Variation database stores data imported from external sources and also data calculated on site.
- Data imported from external sources (dbSNP, Sanger, DGVa, ...):
- Variations (SNPs, in-dels, insertion, deletion, ...)
- Structural variations (copy number variation, tandem duplication, inversion, ...)
- Probes for copy number variations
- Locations for variations and structural variations
- Alleles
- Populations
- Genotypes
- Phenotypes
- Calculated data: see the Predicted data page.
Variation classes
We call the class of a variation according to its component alleles and its mapping to the reference genome, and then display this information on the website. Internally we use Sequence Ontology terms, but we map these to our own 'display' terms where common usage differs from the SO definition (e.g. our term SNP is closer to the SO term SNV). All the classes we call, along with their equivalent SO term are shown in the table below. We also differentiate somatic mutations from germline variations in the display term, prefixing the term with 'somatic'. API users can fetch either the SO term or the display term.
* | Ensembl term | SO term | SO description | SO accession | Called for |
---|---|---|---|---|---|
SNP | SNV | SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. | SO:0001483 | Variation | |
somatic_SNV | |||||
indel | indel | A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. | SO:1000032 | Variation | |
somatic_indel | |||||
substitution | substitution | A sequence alteration where the length of the change in the variant is the same as that of the reference. | SO:1000002 | Variation | |
somatic_substitution | |||||
tandem_repeat | tandem_repeat | Two or more adjcent copies of a region (of length greater than 1). | SO:0000705 | Variation | |
somatic_tandem_repeat | |||||
Complex | complex_structural_alteration | A structural sequence alteration or rearrangement encompassing one or more genome fragments. | SO:0001784 | Structural variation | |
somatic_Complex | |||||
Gain | copy_number_gain | A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. | SO:0001742 | Structural variation | |
somatic_Gain | |||||
Loss | copy_number_loss | A sequence alteration whereby the copy number of a given region is less than the reference sequence. | SO:0001743 | Structural variation | |
somatic_Loss | |||||
CNV | copy_number_variation | A variation that increases or decreases the copy number of a given region. | SO:0001019 | Structural variation | |
somatic_CNV | |||||
Interchromosomal breakpoint | interchromosomal_breakpoint | A rearrangement breakpoint between two different chromosomes. | SO:0001873 | Structural variation | |
somatic_Interchromosomal breakpoint | |||||
Intrachromosomal breakpoint | intrachromosomal_breakpoint | A rearrangement breakpoint within the same chromosome. | SO:0001874 | Structural variation | |
somatic_Intrachromosomal breakpoint | |||||
inversion | inversion | A continuous nucleotide sequence is inverted in the same position. | SO:1000036 | Structural variation | |
somatic_inversion | |||||
Tandem duplication | tandem_duplication | A duplication consisting of 2 identical adjacent regions. | SO:1000173 | Structural variation | |
somatic_Tandem duplication | |||||
translocation | translocation | A region of nucleotide sequence that has translocated to a new position. | SO:0000199 | Structural variation | |
somatic_translocation | |||||
deletion | deletion | The point at which one or more contiguous nucleotides were excised. | SO:0000159 | Variation Structural variation |
|
somatic_deletion | |||||
insertion | insertion | The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. | SO:0000667 | Variation Structural variation |
|
somatic_insertion | |||||
sequence_alteration | sequence_alteration | A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. | SO:0001059 | Variation Structural variation |
|
somatic_sequence_alteration |
* Corresponding colours in the Genome browser (only for Structural variations). The colours are based on the dbVar displays.
Insertion and Deletion coordinates
In Ensembl, an insertion is indicated by start coordinate = end coordinate + 1. For example, an insertion of 'C' between nucleotides 12600 and 12601 on the forward strand is indicated with start and end coordinates as follows:
12601 12600
A deletion is indicated by the exact nucleotide coordinates. For example, a three base pair deletion of nucleotides 12600, 12601, and 12602 of the reverse strand will have start and end coordinates of :
12600 12602
Variation sets
We use the concept of variation sets to group variations that share some property together. For example, we have grouped the variations identified in the three different 1000 Genomes pilot studies into separate variation sets. The sets can be further subdivided into supersets and subsets to reflect hierarchical relationships between them. In the case of the 1000 Genomes pilot sets, these are divided into subsets based on population. For example, the set representing variations identified in the first 1000 Genomes pilot study is named '1000 Genomes - Low coverage' and has three subsets: '1000 Genomes - Low coverage - CEU', '1000 Genomes - Low coverage - CHB+JPT' and '1000 Genomes - Low coverage - YRI'. The variation sets can be displayed as separate tracks on the location view. This behaviour is controlled from the 'Germline variations' section on the configuration panel which is accessed by clicking the 'Configure this page' link in the left hand side navigation.
The sets are constructed during production and are stored in the database. The table below lists the available variation sets in the Ensembl variation database (subsets are indicated by bullet points).
Variation sets common to all the species
Name | Short name | Description |
---|---|---|
All failed variations | fail_all | Variations that have failed the Ensembl QC checks |
Variation sets specific to Human
Name | Short name | Description |
---|---|---|
1000 Genomes - All | 1kg | Variants genotyped by the 1000 Genomes project (phase 1) |
|
1kg_afr | Variants genotyped in African individuals by the 1000 Genomes project (phase 1) |
|
1kg_afr_com | Variants genotyped in African individuals by the 1000 Genomes project (phase 1) with frequency of at least 1% |
|
1kg_amr | Variants genotyped in admixed American individuals by the 1000 Genomes project (phase 1) |
|
1kg_amr_com | Variants genotyped in admixed American individuals by the 1000 Genomes project (phase 1) with frequency of at least 1% |
|
1kg_asn | Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 1) |
|
1kg_asn_com | Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 1) with frequency of at least 1% |
|
1kg_com | Variants genotyped by the 1000 Genomes project (phase 1) with frequency of at least 1% |
|
1kg_eur | Variants genotyped in European individuals by the 1000 Genomes project (phase 1) |
|
1kg_eur_com | Variants genotyped in European individuals by the 1000 Genomes project (phase 1) with frequency of at least 1% |
1000 Genomes - High coverage - Trios | 1kg_hct | Variations called by the 1000 Genomes project on high coverage sequence data from two family trios (Pilot 2) |
1000 Genomes - Low coverage | 1kg_lc | Variations called by the 1000 Genomes project on low coverage sequence data from 179 unrelated individuals (Pilot 1) |
All phenotype-associated variants | ph_variants | Variants that have been associated with a phenotype |
|
ph_cosmic | Phenotype annotations of somatic mutations found in human cancers from the COSMIC project |
|
ph_hgmd_pub | Variants with phenotypes annotated by HGMD |
|
ph_johnson_et_al | Johnson & O'Donnell 'An Open Access Database of Genome-wide Association Results' PMID:19161620 |
|
ph_nhgri | Variants associated with phenotype data from the NHGRI GWAS catalog [http://www.genome.gov/gwastudies/] |
|
ph_omim | Variations linked to entries in the Online Mendelian Inheritance in Man (OMIM) database |
|
ph_uniprot | Variations with phenotype annotations provided by Uniprot |
Anonymous Irish Male | ind_irish | Variants genotyped in an anonymous Irish Male |
Anonymous Korean | ind_ak1 | Variants genotyped in an anonymous Korean individual |
Clinical/LSDB variations from dbSNP | precious | Variations that belong to a reserved or "precious" set of clinically associated SNPs from dbSNP [http://www.ncbi.nlm.nih.gov/projects/SNP/] |
ENSEMBL:Venter | ind_venter | Variants genotyped in Craig Venter |
ENSEMBL:Watson | ind_watson | Variants genotyped in James Watson |
HapMap | hapmap | Variations which have been assayed by The International HapMap Project [http://hapmap.ncbi.nlm.nih.gov/] |
|
hapmap_ceu | Variations which have been assayed by The International HapMap Project from CEU individuals |
|
hapmap_hcb | Variations which have been assayed by The International HapMap Project from HCB individuals |
|
hapmap_jpt | Variations which have been assayed by The International HapMap Project from JPT individuals |
|
hapmap_yri | Variations which have been assayed by The International HapMap Project from YRI individuals |
Henry Louis Gates Jr | ind_gates_jr | Variants genotyped in Henry Louis Gates Jr |
Henry Louis Gates Sr | ind_gates_sr | Variants genotyped in Henry Louis Gates Sr |
Marjolein Kriek | ind_kriek | Variants genotyped in Marjolein Kriek |
Misha Angrist | ind_angrist | Variants genotyped in Misha Angrist |
Rosalynn Gill | ind_gill | Variants genotyped in Rosalynn Gill |
Saqqaq | ind_saqqaq | Variants genotyped in a Palaeo-Eskimo Saqqaq individual |
Saqqaq HC | ind_saqqaq_hc | Variants genotyped in a Palaeo-Eskimo Saqqaq individual (high confidence SNPs) |
Seong-Jin Kim | ind_sjk | Variants genotyped in Seong-Jin Kim |
Stephen Quake | ind_quake | Variants genotyped in Stephen Quake |
YanHang | ind_yh | Variants genotyped in a Han Chinese individual (YanHuang Project) |