Export structural variants
You can use BioMart to query variants, not just genes. (Make sure you use the right Datasets.)
(a) Export the study accession, source name, chromosome, sequence region start and end (in bp) of human structural variations (SV) on chromosome 1, starting at 10,000,000 and ending at 50,000,000.
(b) In a new BioMart query, find the alleles, phenotype descriptions, and associated genes for the human SNPs rs41018921 and rs500510987. Can you view this same information in the Ensembl browser?
(a) Choose Ensembl Variation and Danio rerio Structural Variation.
Filters: Region: Chromosome 1, Base pair start: 10000000, Base pair end: 50000000
Count shows 162 structural variants.
Attributes: Structural Variation (SV) Information: DGVa Study Accession and Source Name, Structural Variation (SV) Location: Chromosome/scaffold name, Chromosome/scaffold position start (bp) and Chromosome/scaffold position start (bp) end (bp).
(b) Choose Ensembl Variation and Danio rerio Short Variation (SNPs and indels).
Filters: Filter by Variation name enter: rs41018921, rs500510987
Attributes: Variant Name, Variant Alleles, Phenotype description and Associated gene.
You can view this same information in the Ensembl browser. Click on one of the variation IDs (names) in the result table. The variation tab should open in the Ensembl browser. Click Phenotype Data.
