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SNP rsid by location?

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?

snp
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updated by sk792 • sk792 • written by Agatha • Agatha

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

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written by charleyfarley • charleyfarley

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)

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written by fo3c fo3c

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.

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written by Peixe Peixe

2 answers

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 |
+-------------+
• 129 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks. It works nicely.

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written by Agatha • Agatha

@Peixe very important indeed. Thank you.

• 235 views • link
written by Agatha • Agatha

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

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written by sk792 • sk792

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