VEP for chicken data
We have identified a few variants associated with body size in chicken (bGalGal1.mat.broiler.GRCg7b):
chr 6, genomic coordinate 23650222, alleles A/C, forward strand
chr 6, genomic coordinate 23645685, alleles C/A, forward strand
chr 1, genomic coordinate 51237121, alleles C/T, forward strand
(a) Which genes and transcripts do these variants map to?
(b) What are the consequence terms for these variants?
(c) Which regulatory feature is affected by the variants?
Go to the Variant Effect Predictor (VEP) under Tools on the top banner of any Ensembl page.
Copy the following into the Paste data text box: 6 23650222 23650222 A/C + var1, 6 23645685 23645685 C/A + var2, 1 51237121 51237121 C/T + var3,
Note that this is the Ensembl default format (chr start end reference/alternate alleles). For additional formats accepted by VEP, have a look here: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
Click Run.
(a) In the Results table, you’ll see that the variants fall into three genes.
(b) The consequence terms are listed in the Consequence column and Consequences (all) chart and include intron_variant, regulatory_region_variant, upstream_gene_variant and downstream_gene_variant.
(c) Variant 3 at 1:51237121-51237121 with T allele affects regulatory feature ENSR00000006264 (promoter).
