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. 2018 Jan 1:2018:bay119.
doi: 10.1093/database/bay119.

Ensembl variation resources

Sarah E Hunt  1 , William McLaren  1 , Laurent Gil  1 , Anja Thormann  1 , Helen Schuilenburg  1 , Dan Sheppard  1 , Andrew Parton  1 , Irina M Armean  1 , Stephen J Trevanion  1 , Paul Flicek  1 , Fiona Cunningham  1
Affiliations

Ensembl variation resources

Sarah E Hunt et al. Database (Oxford). .

Abstract

The major goal of sequencing humans and many other species is to understand the link between genomic variation, phenotype and disease. There are numerous valuable and well-established variation resources, but collating and making sense of non-homogeneous, often large-scale data sets from disparate sources remains a challenge. Without a systematic catalogue of these data and appropriate query and annotation tools, understanding the genome sequence of an individual and assessing their disease risk is impossible. In Ensembl, we substantially solve this problem: we develop methods to facilitate data integration and broad access; aggregate information in a consistent manner and make it available a variety of standard formats, both visually and programmatically; build analysis pipelines to compare variants to comprehensive genomic annotation sets; and make all tools and data publicly available.

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Figures

Figure 1
Figure 1
A variant summary view for rs148698650 that displays the global minor allele frequency from the 1000 Genomes Project, other variants at the same location and links to projects providing additional information about the variant. URL: https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=rs148698650
Figure 2
Figure 2
The ‘Region in detail’ view showing 5 of the available 66 tracks of variant data. URL: https://www.ensembl.org/Homo_sapiens/Location/View?r=10:79069035-79316528
Figure 3
Figure 3
Displays of the frequency spectrum of variant rs1333049 in the 1000 Genomes Project and Genome Aggregation Database panels. URL: https://www.ensembl.org/Homo_sapiens/Variation/Population?v=rs1333049
Figure 4
Figure 4
Transcripts and regulatory features overlapping SV nsv916030. URL: https://www.ensembl.org/Homo_sapiens/StructuralVariation/Mappings?sv=nsv916030
Figure 5
Figure 5
A phenotype table showing variants associated with deafness. URL: https://www.ensembl.org/Homo_sapiens/Phenotype/Locations?oa=EFO:0001063
Figure 6
Figure 6
Part of a table showing predicted consequences for the variants overlapping transcript ENST00000323022.9. Table of transcripts overlapping variant rs143938580. URLs: https://www.ensembl.org/Homo_sapiens/Transcript/Variation_Transcript/Table?t=ENST00000323022, https://www.ensembl.org/Homo_sapiens/Variation/Mappings?v=rs143938580
Figure 7
Figure 7
LD results for a variant can be viewed adjacent to gene structure in both Manhattan and Haploview style plots. URL: https://www.ensembl.org/Homo_sapiens/Variation/LDPlot? v=rs2977605;pop1=373537
See this image and copyright information in PMC

References

    1. Trynka G., Hunt K.A., Bockett N.A. et al. (2011) Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat. Genet., 43, 1193–1201. - PMC - PubMed
    1. Bourgeois S., Jorgensen A., Zhang E.J. et al. (2016) Multi-factorial analysis of response to warfarin in a UK prospective cohort. Genome Med., 8, 2. - PMC - PubMed
    1. von Holdt B.M., Shuldiner E., Koch I.J. et al. (2017) Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. Sci. Adv., 3, e1700398.10.1126/sciadv.1700398. - DOI - PMC - PubMed
    1. Scheben A., Batley J. and Edwards D. (2017) Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol. J., 15, 149–161. - PMC - PubMed
    1. Metzger J., Karwath M., Tonda R. et al. (2015) Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses. BMC Genomics, 16, 764. - PMC - PubMed

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