Index of /centisnps/anno

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[   ]OpenChromDnaseGm19239.annot.gz26-Jul-2016 15:52 2.5M 
[   ]OpenChromDnaseHepg2.annot.gz26-Jul-2016 15:53 1.8M 

Description:

These folder contains the annotations derived in [2] and in the format that 
is used by DAP [1] and TORUS (https://github.com/xqwen/dap/tree/master/torus_src)  

OpenChromDnaseGm19239.annot.gz  ## Annotates the LCL cell-line
OpenChromDnaseHepg2.annot.gz	## Annotates HepG2

The first column annotates the SNP id as it is now used in the GTEx project. 
The second column is categorical: 
    1) footprint-SNP that is not effect-SNP
    2) effect-SNP, also called as binding variant in [1]

Note that if a SNP is not in 1 or 2, it is assumed to be category 0.


Citations:

1: Wen X, Lee Y, Luca F, Pique-Regi R. Efficient Integrative Multi-SNP
Association Analysis via Deterministic Approximation of Posteriors. Am J Hum
Genet. 2016 Jun 2;98(6):1114-29. doi: 10.1016/j.ajhg.2016.03.029. Epub 2016 May
26. PubMed PMID: 27236919; PubMed Central PMCID: PMC4908152.


2: Moyerbrailean GA, Kalita CA, Harvey CT, Wen X, Luca F, Pique-Regi R. Which
Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding? PLoS 
Genet. 2016 Feb 22;12(2):e1005875. doi: 10.1371/journal.pgen.1005875. eCollection
2016 Feb. PubMed PMID: 26901046; PubMed Central PMCID: PMC4764260.