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