This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how to find snps in the 25kb upstream and downstream of one gene

Hello everyone. Thanks for your time.

I have already found all the snps in the gene region on NCBI.And I think maybe the upstream and downstream of the gene are also important. But I have no idea about how to find them.Additionally, I also hope they have the value of MAF.

So who knows how to find snps in the 25kb upstream and downstream of one gene?

Thanks so much!

snp gene database
• 3,047 views • link
updated by Ram Ram • written by shangzhener • shangzhener

Thanks so much for the advice above.

And I am confused why I can't upvote it. The button isn't useful.

• 0 views • link
written by shangzhener • shangzhener

The button should upvote? It works for me - as the thread starter you can also "accept" an answer similar to StackOverflow

• 0 views • link
updated by Ram Ram • written by Philipp Bayer Philipp Bayer

1 answer

There are several ways to do this, so you might consider different options.

One way to do this involves using two R packages:

  1. mygene

  2. proxysnps

    library(mygene) library(proxysnps)

    g <- query(q="NONO", fields="genomic_pos,entrezgene,symbol") v <- get_vcf( chrom = g$hits$genomic_pos$chr[1], start = g$hits$genomic_pos$start[1] - 25e3, end = g$hits$genomic_pos$start[1])

    v$meta[1:5,]

Output:

  CHROM      POS          ID REF ALT QUAL FILTER INFO
1     X 71258496 rs190370246   T   A    .   PASS    .
2     X 71258714  rs73635610   T   C    .   PASS    .
3     X 71258857           .   A  AG    .   PASS    .
4     X 71258914           .   T   C    .   PASS    .
5     X 71258927           .   C   T    .   PASS    .

Another way to do this might be to query the UCSC MySQL database. See these posts to get some hints about how to do that:

• 0 views • link
updated by Ram Ram • written by Kamil Kamil

Log in to answer this question.

More posts like this