[Genome] func column in snp126 table

[Ann Zweig]

Hello Amit,

	You can find this on the SNP details page.

Function: Predicted functional role (each variant may have more than one 
functional role)

     * Locus Region - variation within 2000 bases of gene, but not in transcript
     * Coding - Synonymous - no change in peptide for allele with respect to 
reference assembly
     * Coding - Non-Synonymous - change in peptide for allele with respect to 
reference assembly
     * Untranslated - variation in transcript, but not in coding region interval
     * Intron - variation in intron, but not in first two or last two bases of 
intron
     * Splice Site - variation in first two or last two bases of intron
     * Reference - allele observed in a coding region of the reference sequence
     * Unknown - no known functional classification


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


Amit Indap wrote:
> Hi UCSC
> 
> I was trying to look in the mailing list archives and
> dbSNP page on explanations for some of the functional
> classes of snps. I'm a bit confused about what 
> 
> unknown, locus, coding, and cds-reference mean. 
> If it were coding, you would be able to classify the
> snp as coding-synonymous or coding-nonsynon. I'm
> guessing unknown means intergenic. 
> 
> If you can point me to some documentation that helps
> explain these classifications that would be great!
> 
> Thanks,
> 
> Amit Indap
> Cornell University
> 
> 
>  
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