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

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