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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 130,408 and ending at 210,597.

(b) In a new BioMart query, find the alleles, phenotype descriptions, and associated genes for the human SNPs rs566014072 and rs754099015. Can you view this same information in the Ensembl browser?

(a) Choose Ensembl Variation and Human Structural Variants (GRCh38).

Filters: Region: Chromosome 1, Base pair start: 130408, Base pair end: 210597

Count shows 87 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 Human Short Variation (SNPs and indels) (GRCh38).

Filters: Filter by Variation name enter: rs566014072, rs754099015

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.