[Genome] SNP Function identification - possible error

[Pauline Fujita]

Hello Stephen,

The developer that created this track had the following comment in 
response to your question:

I clicked into a SNP in an exon of BRCA1 (the first match, on chr17), 
rs1800704, and indeed it has both missense (which implies coding) and 
intron in its function list.  However, clicking through to the NCBI 
SNP details page:

http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1800704

-- scroll down until you see a bunch of coral rows with a few yellow 
rows interspersed.  At the same genomic position, the SNP alleles' 
functions are annotated with respect to various RefSeq IDs.  Most are 
exonic but there are a few RefSeqs that have an intron there.  You can 
see that in the RefSeq Genes track too.  

The coloring reflects only the coding functions because there is a 
color priority order (red > green > blue > gray > black).  Coding 
non-synon is red and intron is black; red overrides all other colors, 
and black is overridden by any other color.  The colors can be changed 
in the track controls page to change the relative priority of the 
different functions that may be assigned to the same SNP.  

At chr17:38,487,901-38,488,200 there is a small exon shared by all 
RefSeq Genes; I checked the few SNPs there and none have intron in 
their annotated function list.  

Hopefully this information was helpful and answers your question. If you 
have further questions or require clarification feel free to contact the 
mailing list at genome at soe.ucsc.edu.


Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu






Stephen Lillioja wrote:
> I've been looking at the SNPs for the BRCA1 gene on chromosome 17. The SNPs
> seem to be colour coded OK but when you look at the individual SNP under
> 'Function' they all say they are 'untranslated, intron', I'm sure there must
> be an error here.
>
>  
>
> Regards,
>
>  
>
> Stephen Lillioja 
> Stephen Lillioja MB ChB(Otago) MD (UNSW) FRACP Grad Cert H Ed 
> Professor, Health and Behavioural Sciences 
> Professor, Graduate School of Medicine 
> Faculty of Health and Behavioural Sciences, 
> University of Wollongong 
> Northfields Avenue, 
> Wollongong NSW 2522 
> Australia 
> phone: 61 2 4221 5055 
> FAX:    61 2 4221 5850 
> Mobile: 0419 780 826 
> email:  <mailto:lillioja at uow.edu.au> lillioja at uow.edu.au 
>
>  
>
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