[Genome] dbSNP track on Genome Browser

[Heather Trumbower]

Praveen:

As documented in the track description for our SNP track, our specific 
data sources are the dbSNP tables b126_SNPContigLoc_36_1.bcp.gz, 
b126_SNPMapInfo_36_1.bcp.gz, SNP.bcp.gz 
and b126_SNPContigLocusId_36_1.bcp.gz.    They are available at 
ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data.

I believe NCBI has updated these files at least twice since their first 
release.   We built our track using the initial release in June 2006.
rs41269629 was not included in the June 2006 files.

In Sept. 2006, we worked with Michael Kholodov from dbSNP to 
obtain a new version of the SNPContigLocusId_36_1.bcp.gz file.   This
contained updated functional assignments, and we were able to update
our SNP track to include those updates.

I do not recall whether b126_SNPContigLoc_36_1.bcp.gz was also updated in 
Sept. 2006, but it is possible that rs41269629 was added at that time.
SNPContigLoc is the most fundamental of the dbSNP tables.   Our track 
contains all data from SNPContigLoc that is mapped to the reference with 
weight of 1,2,3.

ftp.ncbi.nih.gov currently has versions of these files dated March 2007.
Our strategy regarding the latest data release is to move forward to use 
the b127*36_2 files.   These have been loaded into a track called SNPs (127),
available at http://genome-test.cse.ucsc.edu.   rs41269629 is included in
that track.

Another alternative for you would be to BLAT the rs41269629 flanking 
sequences.

Please let me know if you have further questions/suggestions regarding 
this issue.   We apologize for any inconvenience we've caused you.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Mon, 9 Apr 2007, Praveen Sethupathy wrote:

> Hello,
>
> The SNP rs41269629 is found in dbSNP's build 126 database, but cannot be
> located in the dbSNP build 126 track of the UCSC Genome Browser. Please
> advise as to why this is the case?  I have contacted NCBI about this, but
> they indicated that I should contact you since you upload their data
> directly as tracks.  Thank you!
>
> Best,
> Praveen
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