Question: Snp Rsid By Location?
4
gravatar for Agatha
6.2 years ago by
Agatha340
Agatha340 wrote:

I have a list of SNPs and their exact locations :

SNP_nr Chromosome Location

 1           1                11088169

How can I get their associated rsIDs programmatically or otherwise?

Thanks.

snp • 6.1k views
ADD COMMENTlink modified 6.2 years ago by charleyfarley0 • written 6.2 years ago by Agatha340

For someone who doesn't use mysql - are there ways to batch submit genome positions and get RSids back this way?

ADD REPLYlink written 6.2 years ago by charleyfarley0
2

Please, do not ask questions in the answers section. If your question is related, just write that as a comment, or a new question if needed.

ADD REPLYlink written 6.2 years ago by Peixe580

If all on the same chromosome you could do something like: select chromStart, name from snp137 where chrom='chr1' and chromStart in (10144,12456,55648)

ADD REPLYlink written 6.2 years ago by fo3c420
6
gravatar for Pierre Lindenbaum
6.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

many answers on biostars , search for UCSC/mysql/api.

eg:

Is there such a thing as a UCSC API?

direct acces to mysql: (slow, because it doesn't use the 'bin' index)

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -Dhg19  -e "select name from snp137 where chrom='chr1' and chromStart=10144"
+-------------+
| name        |
+-------------+
| rs144773400 |
+-------------+
ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Pierre Lindenbaum119k
4

Maybe this is important... On another issue, Get Snp Position From A Python Interface. @Pierre, answered me a similar question with th UCSC API, and the position of the SNP was the chromEnd, or the chromStart+1... If you check the position of this SNP here http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=144773400 you can see that the position is actually 10145...

ADD REPLYlink written 6.2 years ago by Peixe580
2

@Peixe very important indeed. Thank you.

ADD REPLYlink written 6.2 years ago by Agatha340
1

Thanks. It works nicely.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Agatha340
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 672 users visited in the last hour