New URL: http://coetzeeseq.usc.edu/publication/Coetzee_SG_et_al_2012/

Abstract/Summary:
Single nucleotide polymorphisms (SNPs) are increasingly used to tag genetic loci
associated with phenotypes such as risk of complex diseases. Technically, this
is done genome-wide without prior restriction or knowledge of biological
feasibility in scans referred to as genome-wide association studies (GWAS).
Depending on the linkage-disequilibrium (LD) structure at a particular locus,
such tagSNPs may be surrogates for many thousands of other SNPs, and it is
difficult to distinguish those that may play a functional role in the phenotype
from those simply genetically linked. Because a large proportion of tagSNPs have
been identified within non-coding regions of the genome, distinguishing
functional from non-functional SNPs has been an even greater challenge. A
strategy was recently proposed that prioritizes surrogate SNPs based on
non-coding chromatin and epigenomic mapping techniques that have become feasible
with the advent of massively parallel sequencing. Here we introduce an
R/Bioconductor software package that enables the identification of candidate
functional SNPs by integrating information from tagSNP locations, lists of
linked SNPs from the 1000 genomes project, and locations of chromatin features
which may have functional significance. Availability: FunciSNP is available from
Bioconductor (bioconductor.org). 

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May 17, 2012 - Repo made public.

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May 13, 2012 - FunciSNP manuscript accepted in Nucleic Acids Research.
doi: 10.1093/nar/gks542

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Feb 3, 2012 - Reorganized folder project. Added new versions of FunciSNP.

new version of TSS.human.GRCh37
from genomebrowser on 2012-03-26 
filtered only rows with "hg19.knonwCanonical.transcript" != "na"
no duplicated ensembl id's allowed no "na" ensembl id's allowed

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September 27, 2011
This project contains all the current working in house scripts for the Coetzee Lab.

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Each folder represents one in house script. View README within is folder for more information.