[Genome] Further clarification of "func" definitions

[Kayla Smith]

Hello Teri,

Please see this previously answered mailing list question which talks 
about snp128.func:
https://www.soe.ucsc.edu/pipermail/genome/2008-May/016377.html

It is dbSNP who classifies the snps as the functions you've listed 
below.  Here is their faq on functional classes:

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpsnpfaq.section.Reports.SNP_Class_Definition#Reports.Functional_Class

I hope this helps to point you in the right direction.  Please don't 
hesitate to contact us if you have any further questions.

Kayla Smith
UCSC Genome Bioinformatics Group


Manolio, Teri (NIH/NHGRI) [E] wrote:
> Dear Genome Browser,
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> I'm looking for definitions of the "func" entries and found the query
> and responses to Amit Indap but have a few more questions based on a
> recent download:
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> 
> 1. Does "near-gene-5" mean within 2000 bp of the 5' end, and
> "near-gene-3" mean within 2000 bp of the 3' end?  
> 
> 2. Does "intron,near-gene-3" mean that one submitter located the SNP in
> an intron, and another near-gene-3?
> 
> 3. What does "cds-reference,missense" mean-can a missense mutation be
> synonymous?  Or does this mean that two different submitters called it
> two different things?
> 
> 4. What is the definition of "untranslated-5"-presumably within a
> certain number of basepairs of the transcription start site?
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> 
> Thanks!
> 
>  
> 
> Teri Manolio
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> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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