Question: web interface for getting rsID in dbSNP of some coordinate?
0
gravatar for Tommy Carstensen
4.7 years ago by
United Kingdom
Tommy Carstensen200 wrote:

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?

rsid dbsnp • 1.6k views
ADD COMMENTlink modified 4.7 years ago by Pierre Lindenbaum126k • written 4.7 years ago by Tommy Carstensen200

ncbi dbsnp ?

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum126k
Surprisingly doesn't allow you to search by position.
ADD REPLYlink written 4.7 years ago by Tommy Carstensen200

UCSC genome browser with dbSNP version of interest selected among Variation tracks?

ADD REPLYlink written 4.7 years ago by Nicola Casiraghi450
3
gravatar for Pierre Lindenbaum
4.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

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>

 

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Pierre Lindenbaum126k
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