web interface for getting rsID in dbSNP of some coordinate?
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7.0 years ago

When I want to look up an rsID of a genomic coordinate I look in a dbSNP vcf. This is fast, when I have a terminal available and can remember the path to the dbSNP vcf. But does a web interface exist for doing the same task?

dbSNP rsID • 2.7k views
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ncbi dbsnp ?

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Surprisingly doesn't allow you to search by position.
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UCSC genome browser with dbSNP version of interest selected among Variation tracks?

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7.0 years ago

Using dbsnp:

 

http://www.ncbi.nlm.nih.gov/snp/?term=%28%287[Chromosome]%29+AND+57120540%3A57120545[Base+Position]%29+AND+%22homo+sapiens%22[Organism]

using ucsc das:

$ curl "http://genome.ucsc.edu/cgi-bin/das/hg38/features?segment=chr7:57120540,57120543&type=snp142"
<?xml version="1.0" standalone="no"?>
<!DOCTYPE DASGFF SYSTEM "http://www.biodas.org/dtd/dasgff.dtd">
<DASGFF>
<GFF version="1.0" href="http://genome.ucsc.edu/cgi-bin/das/hg38/features">
<SEGMENT id="chr7" start="57120540" stop="57120543" version="1.00" label="chr7">
<FEATURE id="rs374013882.chr7.57120540" label="rs374013882">
 <TYPE id="snp142" category="variation" reference="no">snp142</TYPE>
 <METHOD></METHOD>
 <START>57120541</START>
 <END>57120541</END>
 <SCORE>0</SCORE>
 <ORIENTATION>+</ORIENTATION>
 <PHASE>-</PHASE>
 <GROUP id="rs374013882.chr7.57120540">
  <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:57120540-57120541&amp;db=hg38">Link to UCSC Browser</LINK>
 </GROUP>
</FEATURE>
<FEATURE id="rs142012190.chr7.57120541" label="rs142012190">
 <TYPE id="snp142" category="variation" reference="no">snp142</TYPE>
 <METHOD></METHOD>
 <START>57120542</START>
 <END>57120542</END>
 <SCORE>0</SCORE>
 <ORIENTATION>+</ORIENTATION>
 <PHASE>-</PHASE>
 <GROUP id="rs142012190.chr7.57120541">
  <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:57120541-57120542&amp;db=hg38">Link to UCSC Browser</LINK>
 </GROUP>
</FEATURE>
</SEGMENT>
</GFF></DASGFF>

 

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