Integrative analysis across 3,604 GWAS reveals multiple novel cell type-specific regulatory associations

<p>This dataset contains files associated with the manuscript &quot;Integrative analysis across 3,604 GWAS reveals multiple novel cell type-specific regulatory associations&quot;. This manuscript presents Functional element Overlap analysis of the Results of GWAS Experiments 2 (FORGE2), a new method for detecting key phenotype-associated tissues, cell types and regulatory elements using GWAS summary statistics. This manuscript also presents FORGE2 results across several thousand GWAS.</p> <p>&nbsp;</p> <p>FORGE2 code (as of 22 November 2021) is contained in the compressed folder FORGE2.zip.</p> <p>FORGE2 code is also contained on GitHub at https://github.com/charlesbreeze/FORGE2</p> <p>&nbsp;</p> <p>The main figures for the FORGE2 paper, covering the main elements of FORGE2 analysis and results, are:</p> <ul> <li>Figure1.forge2.DHS.pdf</li> <li>Figure2.forge2.histone.marks.pdf</li> <li>Figure3.histone.mark.comparison.pdf</li> <li>Figure4.forge2.chr.states.pdf</li> <li>Figure5.forge2.relationship.between.marks.pdf</li> <li>Figure6.example.analysis.figure.pdf</li> </ul> <p>&nbsp;</p> <p>Legends for all figures and tables are included in the file FORGE2.legends.for.figures.and.tables.pdf</p> <p>&nbsp;</p> <p>The supplementary figures for the FORGE2 paper, covering additional elements of FORGE2 analysis and results, are:</p> <ul> <li>FigureS1.pdf</li> <li>FigureS2.erc.pdf</li> <li>FigureS3.encode.pdf</li> <li>FigureS4.blueprint.pdf</li> <li>FigureS5.H3K4me1.pdf</li> <li>FigureS6.H3K4me3.pdf</li> <li>FigureS7.H3K36me3.pdf</li> <li>FigureS8.H3K27me3.pdf</li> <li>FigureS9.H3K9me3.pdf</li> <li>FigureS10.upset.plot.histone.marks.pdf</li> <li>FigureS11.TssA.pdf</li> <li>FigureS12.TssAFlnk.pdf</li> <li>FigureS13.TssBiv.pdf</li> <li>FigureS14.Tx.pdf</li> <li>FigureS15.TxFlnk.pdf</li> <li>FigureS16.TxWk.pdf</li> <li>FigureS17.ZNF-Rpts.pdf</li> <li>FigureS18.BivFlnk.pdf</li> <li>FigureS19.Enh.pdf</li> <li>FigureS20.EnhBiv.pdf</li> <li>FigureS21.EnhG.pdf</li> <li>FigureS22.Het.pdf</li> <li>FigureS23.Quies.pdf</li> <li>FigureS24.ReprPC.pdf</li> <li>FigureS25.ReprPCWk.pdf</li> <li>FigureS26.upset.plot.chromatin.states.pdf</li> </ul> <p>&nbsp;</p> <p>The supplementary tables for the FORGE2 paper, with additional data regarding FORGE2 analysis and results, are:</p> <ul> <li>Table.S1.erc2.DHS.xlsx</li> <li>Table.S2.erc.xlsx</li> <li>Table.S3.encode.xlsx</li> <li>Table.S4.blueprint.xlsx</li> <li>Table.S5.H3K4me1.xlsx</li> <li>Table.S6.H3K4me3.xlsx</li> <li>Table.S7.H3K36me3.xlsx</li> <li>Table.S8.H3K27me3.xlsx</li> <li>Table.S9.H3K9me3.xlsx</li> <li>Table.S10.chrstate15.xlsx</li> <li>Table.S11.MPNs_example.analysis.forge2.h3.all.xlsx</li> <li>Table.S12.MPNs_example.analysis.forge2.dhs.xlsx</li> </ul> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p>