how to find snps in the 25kb upstream and downstream of one gene

Question

[shangzhener]

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!

[shangzhener]

Thanks so much for the advice above.

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

[Philipp Bayer]

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

Answer 1

[Kamil]

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:

• Snp Query From Ucsc
• How To Map A Snp To A Gene Around +/- 60Kb ?