Combining SNP-to-gene linking strategies to pinpoint disease genes and assess disease omnigenicity
Creators: name: Gazal Steven
Publisher: name: Zenodo
Year: 2023

description: Datasets and codes to replicate the results and Figures of "Combining SNP-to-gene linking strategies to pinpoint disease genes and assess disease omnigenicity".
#baselineS2Gannots.tgzThis compressed file contains S2G-derived and cS2G SNP annotations and LD scores for critical gene sets and all genes.This compressed file contains s-ldsc outputs of the baseline-S2G model and the baseline-S2G model with the cS2G-derived SNP annotation.
#cS2G_1000GEUR.zipThis compressed file contains cS2G scores for 9,997,231 SNPs with a minor allele count >=5 in a 1000 Genomes Project European reference panel (same as reference SNPs used in S-LDSC) (see file allsnps.txt.gz for a complet list).SNP: SNP IDGENE: GENE IDcS2G: cS2G scoreINFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)
#cS2G_UKBB.zipThis compressed file contains cS2G scores for 19,476,620 SNPs with a minor allele count>=0.1% in the UK Biobank (see file allsnps.txt.gz for a complet list).SNP: SNP IDGENE: GENE IDcS2G: cS2G scoreINFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)
#code.zipThis compressed file contain codes to replicate the results of Gazal et al. 2022 Nat GenetThis file has been updated on 8/28/23 with new links to https://zenodo.org/record/8292725
#critical_gene_sets.zipThis compressed file contains genes of critical gene setslist_genes_qc.txt.gz: contains information on all the 19,995 genes analyzedtraining_constrained_conserved.txt.gz: training critical gene set; contains list of genes with constrained exons and conserved promotersvalidation_popsexopro_*: validation critical gene sets; contain list of genes with highest pops score
#figures_paper.zipThis compressed file contains the code (figures.r) and datasets (figure*txt) to reproduce figures of the paper
#finemapping_cS2G_UKBB.zipThis compressed file contains cS2G score for 138,716 potentially causal SNP-gene-disease triplets inferred from causal SNP-disease pairs with PIP>0.05 from functionally informed fine-mapping of 49 UK Biobank diseases/traits.CHR: ChromosomeBP: Position (hg19)SNP: SNP IDDISEASE.TRAIT: PHENOTYPEPIP: Posterior inclusion probabilityGENE: Gene IDcS2G: cS2G scoreINFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)This compressed file also contains a beta2 directory with PolyFun outputs for each traits (used in the omnigenicity analyses)
#gwas_catalog_cS2G.zipThis compressed file contains cS2G score for 78,499 potentially causal SNP-gene-disease triplets from the NHGRI-EBI GWAS catalog (accessed file: gwas_catalog_v1.0-associations_e100_r2021-02-25.txt)PUBMEDID: PUBMED IDDISEASE.TRAIT: PHENOTYPECHR: ChromosomePOS: Position (hg19)SNP: SNP IDGENE: Gene IDcS2G: cS2G scoreINFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)
#pergeneh2_cS2G_UKBB.zipThis compressed file contains per gene heritability for 19,995 genes in 49 UK Biobank traitsGENE: name of the geneh2gene: heritability linked to genes using cS2GMgene: sum of the linking scores for SNPs with a beta2>0h2gene_common: heritability of common SNPs linked to genes using cS2GMgene_common: sum of the linking scores for common SNPs with a beta2>0h2gene_lowfreq: heritability of low-frequency SNPs linked to genes using cS2GMgene_lowfreq: sum of the linking scores for low-frequency SNPs with a beta2>0
#S2G_bed.tgzThis compressed file contains bed files for the diverse S2G strategies.#S2G_original.zipThis compressed file contains original S2G startegies that we computed (fine-mapped eQTLs), obtained through personal coomunication (Cicero), or accessed online.
#sumstats_63.zipThis compressed file contains the 63 independent summary statistics, and additional blood/immune traits
#sumstats_UKBB122K.zipThis compressed file contains the 49 UK BiobanK summary statistics computed on N=122K and used in the omnigenicity analyses