<p>Yes, if you load the list you are interested in as a non-indexed "BED" file then you can jump to an rsID or any other name in the BED file. You'll need a targeted list, dbSNP for example is much too large to load in this way.</p>

CC BY-SA 3.0
2017-10-26T09:33:43.600Z
Great, thank. Is there an hg38 bed file with the rsIDs of one of the 1M SNP arrays out in the market?
719016
CC BY-SA 3.0
2017-10-25T18:37:27.600Z
2017-10-25T19:42:00.760Z
2017-10-25T19:42:00.760Z
Jim Robinson
<p>If you want all rsIDs (complete dbSnp database) then Pierre's answer is the best option currently.    Any bed file with all the rsIDs would be too big to load.  For a targeted list of, say, 100,000 or fewer snps you can use a bed file.  </p>

<p>BTW igv.js already does the equivalent of Pierre's suggestion, this will be ported to IGV desktop in the near future.  </p>

CC BY-SA 3.0
2017-10-26T20:05:43.900Z
2017-10-26T20:05:43.900Z
Jim Robinson
<p>you can use mysql ucsc to get the position of the SNP and then ask IGV to take some picures: see <a href="https://software.broadinstitute.org/software/igv/batch" rel="nofollow noreferrer">https://software.broadinstitute.org/software/igv/batch</a></p>

<pre><code>$ echo -e 'rs66823261\nrs25' | awk '{printf("select concat(chrom,\":\",chromStart-10,\"-\",chromEnd+10) from  snp150 where name=\"%s\";\n",$1);}' | mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg38 -N | awk '{printf("goto %s\nsnapshot\n",$1);}'

goto chr8:170681-170702
snapshot
goto chr7:11584131-11584152
snapshot
</code></pre>

CC BY-SA 3.0
2017-10-26T09:49:13.210Z
2017-10-26T09:49:13.210Z
Pierre
<p>Is it possible to load a list of rsID identifiers (e.g. rs66823261) to IGV to then be able to jump to the location of each of them when copy+pasting the rsID on the locus text box?</p>

<p>For human and other genomes, there is currently the feature of typing in a gene name, then jumping to the gene location.</p>

<p>I wonder if there is a way of achieving the same for rsIDs.</p>

<p>EDIT: thanks for the answers so far. I downloaded the Infinium GSA bed file from Illumina's website (<a href="https://support.illumina.com/downloads/infinium-global-screening-array-v1-0-support-files.html" rel="nofollow noreferrer">https://support.illumina.com/downloads/infinium-global-screening-array-v1-0-support-files.html</a>), loaded on an IGV session, which asked to create an index. I did a liftover of the file to hg38 and sorted with bedtools sort. Then I went to the text box, introduced one of the rs ids:</p>

<p>rs6569648</p>

<p>Got a positive result. Thank you all!</p>

<snp><igv>
IGV jump to rsID location
# IGV jump to rsID location

(Asked by: username_0 on 2017-10-25)

Is it possible to load a list of rsID identifiers (e.g. rs66823261) to IGV to then be able to jump to the location of each of them when copy+pasting the rsID on the locus text box?

For human and other genomes, there is currently the feature of typing in a gene name, then jumping to the gene location.

I wonder if there is a way of achieving the same for rsIDs.

EDIT: thanks for the answers so far. I downloaded the Infinium GSA bed file from Illumina's website (<https://support.illumina.com/downloads/infinium-global-screening-array-v1-0-support-files.html>), loaded on an IGV session, which asked to create an index. I did a liftover of the file to hg38 and sorted with bedtools sort. Then I went to the text box, introduced one of the rs ids:

rs6569648

Got a positive result. Thank you all!

**Tags:** snp, igv

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## 3 answers

### Answer by username_1 on 2017-10-25. Score: 2 | Accepted answer

Yes, if you load the list you are interested in as a non-indexed "BED" file then you can jump to an rsID or any other name in the BED file. You'll need a targeted list, dbSNP for example is much too large to load in this way.

> **Comments:**
> **username_0**: Great, thank. Is there an hg38 bed file with the rsIDs of one of the 1M SNP arrays out in the market?  

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### Answer by username_1 on 2017-10-26. Score: 0

If you want all rsIDs (complete dbSnp database) then Pierre's answer is the best option currently. Any bed file with all the rsIDs would be too big to load. For a targeted list of, say, 100,000 or fewer snps you can use a bed file.

BTW igv.js already does the equivalent of Pierre's suggestion, this will be ported to IGV desktop in the near future.


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### Answer by username_2 on 2017-10-26. Score: 0

you can use mysql ucsc to get the position of the SNP and then ask IGV to take some picures: see https://software.broadinstitute.org/software/igv/batch
$ echo -e 'rs66823261\nrs25' | awk '{printf("select concat(chrom,\":\",chromStart-10,\"-\",chromEnd+10) from  snp150 where name=\"%s\";\n",$1);}' | mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg38 -N | awk '{printf("goto %s\nsnapshot\n",$1);}'

goto chr8:170681-170702
snapshot
goto chr7:11584131-11584152
snapshot


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