[Genome] func column in snp126 table

[Heather Trumbower]

Amit:

A few additional comments:

Coding is an older category that dbSNP appears to be moving away from 
using, in favor of coding-synon and coding-nonsynon.   You will find very 
few examples of this in the data (hg18.snp126 for example).

Unknown is in fact intergenic.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Fri, 2 Mar 2007, Ann Zweig wrote:

> 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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