[Genome] Mapping SNP positions and IDs

[Archana Thakkapallayil]

Hello Kiran,

You can extract this information using the Table Browser. The field 
"observed" in the 'snp126' table for hg18 assembly ( table 'snp125' for 
hg17 assembly ), contains information on the sequences of the observed 
alleles from rs-fasta files.

To do this make the following selections in the Table Browser:

clade: vertebrate
genome: human
assembly: Mar. 2006 (or choose May 2004 if that's the database you are
using)
group: variation and repeats
track: SNPs
table: snp126 (or snp125 for the May 2004 database)
region: select the "genome" radio button
identifiers (names/accessions): paste the list of rs numbers here, then 
hit "submit"
output format: choose "selected fields from primary and related tables"
output file: enter a file name here if you wish to save the information 
directly to a file, or leave this blank to view the results in the 
browser window

Hit "get output"

Now you can select the fields in which you are interested; in this case, 
choose "chrom", "chromStart", "chromEnd", "name" and "observed", and hit 
the "get output" button. This gives you the position and allele 
information for all your snp ID's. Be patient, this database table is 
quite large.

You can then take this output and make BED4 custom track to get the 
upstream and downstream sequences. After loading your custom track, 
choose "Custom Tracks" as the group and "sequence" as output format in 
the Table Browser. Then click "get output". On this page under 'Sequence 
Retrieval Region Options' you can specify the number of bases upstream 
and downstream and then hit "get sequence".

Information about creating custom tracks can be obtained here:

http://genome.cse.ucsc.edu/goldenPath/help/customTrack.html

More information on BED format is here:

http://genome.cse.ucsc.edu/goldenPath/help/customTrack.html

I hope this information is helpful to you. If this doesn't answer your 
question completely, please feel free to write back


Regards,

Archana
UCSC Genome Bioinformatics Group


Kiran Annaiah wrote:
> Hello there,
>
>  
>
>  
>
> I am trying to map few of my SNP's and extract 100-200bp upstream and
> downstream of it.
>
> I was able to figure out how do those using your browser. I was also
> able to map other SNP's in the upstream and downstream regions.
>
>  
>
> I am doing this so I can avoid using those regions when designing my
> primer.
>
>  
>
>  
>
> But the one drawback I saw was that (specific to my problem), in the
> fasta sequence file is that, it does not tell me what the rsID's of the
> mapped SNPs. I would also like to know the alleles (example: [a/t]) at
> that particular SNP location.
>
>  
>
> Is there a way I can do this using the browser or atleast submit a batch
> query with my rsID's and obtain all the SNPs which fall within the
> upstream and downstream region of the sequence I need to use for
> designing my primers.
>
>  
>
> The reason I needed the allele info [A/t] at the SNP locations is to
> submit it to a specific machine we use here.
>
>  
>
> Any suggestions and ideas would be great. We have hundreds of SNPS to
> query and would be a pain to do it manually. I AM trying to see if I
> could write a script to automate this process.
>
>  
>
> Thank you
>
>  
>
> Regards
>
> Kiran
>
>  
>
> Dept of Human Genetics
>
> University of Chicago
>
>  
>
> 773-391-1208
>
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>