How to obtain upstream variant genes?

Question

[magnolia]

Hi,

In rs7988901 it says the genes for this variant are:

ZAR1L : Intron Variant

BRCA2 : 2KB Upstream Variant

But position-wise (chr13:32314943 in GRCh38), it's in ZAR1L only since it's not in BRCA2 exactly. How dbSNP determined this? How can I do this for any variant I want?

Thanks a lot!

Answer 1

[barslmn]

You can use VEP. Check out the distance parameter. https://www.ensembl.org/Multi/Tools/VEP?db=core

[magnolia]

Thank you! I'm actually looking for a file to query from. Do you know any? So I can search the position and chromosome, and find all possible consequences.