Search set of SNPs on genome browser by rsid
Hopefully a simple question.
I have a list of SNPs in rs12345 format. I want to visually see these SNPs and their positions on the genome (they are all relatively close to one another, same chromosome). How can I use genome browser to look up a list of SNPs by rsid?
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Pierre Lindenbaum
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lordoftheowl •
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lordoftheowl •
1 answer
create an UCSC custom track with your SNP, and open it in the UCSC browser.
mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg19 -e 'select chrom,chromStart,chromEnd,name from snp150 where name in ("rs1052373574", "rs953910623", "rs766295811", "rs62651026", "rs386641822", "rs145427775", "rs370233998", "rs1008829651", "rs905296478", "rs555500075") ' -N > custom.bed
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One option would be to search the SNP at NCBI. See this example (click on the SNP name to open genome view). You can search with
rsnumber at UCSC.