SNP rsid by location?

Question

[Agatha]

I have a list of SNPs and their exact locations :

SNP_nr Chromosome Location
     1          1 11088169

How can I get their associated rsid programmatically or otherwise?

[charleyfarley]

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

[Peixe]

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.

[fo3c]

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)

Answer 1

[Pierre Lindenbaum]

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 |
+-------------+

[Peixe]

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...

[Agatha]

@Peixe very important indeed. Thank you.

Answer 2

[sk792]

Hi everyone, I have prepared a video on YouTube using Kaviar to show you how to map from Chromosome and Base Pair Information to rsID #s for Single Nucleotide Polymorphisms (SNPs):

For example, how do you go from converting from Genetic Variant at chr1, 715265 to the SNP ID: rs12184267

Please note that a key website used here is: http://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.pl Kaviar's limit is only 100,000 genetic variant Ids in 1 query search at a time.

I hope this helps! Please let me know if you have any questions at all. I hope to help with more videos, so please subscribe to my channel (https://www.youtube.com/channel/UCNhVAcIdarXzTCWZ27N1EmQ) for more updates :)

Best wishes, Saniya Khullar