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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.

Bos taurus [sources] Canis familiaris [sources] Danio rerio [sources] Drosophila melanogaster [sources] Equus caballus [sources]

Felis catus [sources] Gallus gallus [sources] Homo sapiens [sources] Macaca mulatta [sources] NEW! Monodelphis domestica [sources]

Mus musculus [sources] Ornithorhynchus anatinus [sources] Pan troglodytes [sources] Pongo abelii [sources] Rattus norvegicus [sources]

Saccharomyces cerevisiae [sources] Sus scrofa [sources] Taeniopygia guttata [sources] Tetraodon nigroviridis [sources]

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)
1000 Genomes - AFR	1kg_afr	Variants genotyped in African individuals by the 1000 Genomes project (phase 1)
1000 Genomes - AFR - common	1kg_afr_com	Variants genotyped in African individuals by the 1000 Genomes project (phase 1) with frequency of at least 1%
1000 Genomes - AMR	1kg_amr	Variants genotyped in admixed American individuals by the 1000 Genomes project (phase 1)
1000 Genomes - AMR - common	1kg_amr_com	Variants genotyped in admixed American individuals by the 1000 Genomes project (phase 1) with frequency of at least 1%
1000 Genomes - ASN	1kg_asn	Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 1)
1000 Genomes - ASN - common	1kg_asn_com	Variants genotyped in East Asian individuals by the 1000 Genomes project (phase 1) with frequency of at least 1%
1000 Genomes - All - common	1kg_com	Variants genotyped by the 1000 Genomes project (phase 1) with frequency of at least 1%
1000 Genomes - EUR	1kg_eur	Variants genotyped in European individuals by the 1000 Genomes project (phase 1)
1000 Genomes - EUR - common	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
COSMIC phenotype variants	ph_cosmic	Phenotype annotations of somatic mutations found in human cancers from the COSMIC project
HGMD-PUBLIC phenotype variants	ph_hgmd_pub	Variants with phenotypes annotated by HGMD
Johnson & O'Donnell phenotype variants	ph_johnson_et_al	Johnson & O'Donnell 'An Open Access Database of Genome-wide Association Results' PMID:19161620
NHGRI catalog phenotype variants	ph_nhgri	Variants associated with phenotype data from the NHGRI GWAS catalog [http://www.genome.gov/gwastudies/]
OMIM phenotype variants	ph_omim	Variations linked to entries in the Online Mendelian Inheritance in Man (OMIM) database
Uniprot phenotype variants	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	hapmap_ceu	Variations which have been assayed by The International HapMap Project from CEU individuals
HapMap - HCB	hapmap_hcb	Variations which have been assayed by The International HapMap Project from HCB individuals
HapMap - JPT	hapmap_jpt	Variations which have been assayed by The International HapMap Project from JPT individuals
HapMap - YRI	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)