- Course overview
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- Why Ensembl?
- What is Ensembl?
- When to use Ensembl
- How to access Ensembl
- How to search Ensembl
- How to search Ensembl
- How to search Ensembl
- Navigating Ensembl
- Customise Ensembl
- Manage your data
- Export data
- Download data with BioMart
- Bulk download genome-wide data files with FTP
- Ensembl tools
- Summary
- Guided examples of using Ensembl
- Exercises
- Your feedback
- Get help and support on Ensembl
- Acknowledgements
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Sequence variation
The majority of sequence variants in Ensembl are single nucleotide polymorphisms (SNPs), insertions and deletions (indels) imported from NCBI dbSNP and EVA. For human SNPs in particular, we aim to keep current with dbSNP, updating these with every Ensembl release (every 2-3 months). Projects submitting their variants to dbSNP include individual labs, the 1000 Genomes project and gnomAD. Small sequence variants are mapped onto the reference genome, and effects on Ensembl transcripts are determined. Larger structural variations such as copy number variations (CNVs) are also viewable on the genomic sequence. These include structural variants from dGVA and somatic mutations. Watch video (Video 7) to learn how to view SNPs and CNVs in the Ensembl browser.
 Determine the effect of your variants on the Ensembl transcript set using the Variant Effect Predictor tool. |
Genotype and allele frequency information for human variants is imported from dbSNP, and reflects data from sources such as gnomAD and the 1000 Genomes project. Disease and phenotype associations are imported from projects such as the GWAS catalog, ClinVar, OMIM and EGA.
 Learn how to navigate variation views in this section. Read more about variation sources in Ensembl. |