near by genes for Variant

Question

[pragathi.sneha91]

Given a variant(rs ID) , how to find nearby genes of that variant? Any tool/method

[cpad0112]

if you have it as VCF or text, VEP should be able to do that. Option to use is --distance [bp_distance(,downstream_distance_if_different)]

Answer 1

[Jeremy]

I'm not sure if this answers your question, but if you have a gene of interest, you can search for it along with your species of interest in the NCBI Gene database. Then click on the relevant search result and scroll down to "Genomic context", where you will see a chromosomal map of you gene of interest and the closest nearby genes.