Data of GWAS associated SNPs in regulatory regions

posted on 23.01.2015 by Ian Dunham, Eugene Kulesha, Valentina Iotchkova, Sandro Morganella, Ewan Birney

Data file 1: DNase I hotspot samples included in FORGE analysis.

A list of DNase I hotspot samples included in FORGE analysis is shown.The table lists details of the 125 ENCODE and 299 Roadmap Epigenome samples. The fields are File: file name; Lab: data-generating lab. One of UW (University of Washington, John Stamatoyannopoulos lab), Duke:UNC:UTA (Duke University, Greg Crawford lab) or combined representing a merged dataset from both labs; Experiment type: always DNase-seq in the current implementation; Project: Either ENCODE or Roadmap; Cell: cell type; Tissue: tissue name derived as described above; Data type: always hotspots in the current implementation; Short name: a short sample used for plotting; Individual: either the code for the individual sample as described in Biosamples or NA if not available; GEO accession: the GEO accession where found, or “Not found” if it could not be deconvoluted.

Data file 2: List of phenotypes analysed.

The list of phenotypes analysed, with non-redundant SNP counts and Pubmed identifiers for the studies involved is shown. This table is also available in the data directory of the GitHub release,https://github.com/iandunham/Forge.





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