SNP rsid by location?

2

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

• 8.5k views

updated 2 hours ago by

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written 8.5 years ago by

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

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: 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 (www.youtube.com/channel/UCNhVAcIdarXzTCWZ27N1EmQ) for more updates 🙂

Best wishes,
Saniya Khullar


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