Combining SNP-to-gene linking strategies to pinpoint disease genes and assess disease omnigenicity
Creators: name: Gazal Steven
Publisher: name: Zenodo
Year: 2021

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.tgz<br> This compressed file contains S2G-derived and cS2G SNP annotations and LD scores for critical gene sets and all genes.<br> 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.zip<br> This compressed file contains cS2G scores for 9,997,231 SNPs with a minor allele count &gt;=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).<br> SNP: SNP ID<br> GENE: GENE ID<br> cS2G: cS2G score<br> INFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies) #cS2G_UKBB.zip<br> This compressed file contains cS2G scores for 19,476,620 SNPs with a minor allele count Ã¢â€°Â¥0.1% in the UK Biobank (see file allsnps.txt.gz for a complet list).<br> SNP: SNP ID<br> GENE: GENE ID<br> cS2G: cS2G score<br> INFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies) #code.zip<br> This compressed file contain codes to replicate the results of Gazal et al. 2022 Nat Genet #critical_gene_sets.zip<br> This compressed file contains genes of critical gene sets<br> list_genes_qc.txt.gz: contains information on all the 19,995 genes analyzed<br> training_constrained_conserved.txt.gz: training critical gene set; contains list of genes with constrained exons and conserved promoters<br> validation_popsexopro_*: validation critical gene sets; contain list of genes with highest pops score #figures_paper.zip<br> This compressed file contains the code (figures.r) and datasets (figure*txt) to reproduce figures of the paper #finemapping_cS2G_UKBB.zip<br> This compressed file contains cS2G score for 138,716 potentially causal SNP-gene-disease triplets inferred from causal SNP-disease pairs with PIP&gt;0.05 from functionally informed fine-mapping of 49 UK Biobank diseases/traits.<br> CHR: Chromosome<br> BP: Position (hg19)<br> SNP: SNP ID<br> DISEASE.TRAIT: PHENOTYPE<br> PIP: Posterior inclusion probability<br> GENE: Gene ID<br> cS2G: cS2G score<br> INFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies)<br> This compressed file also contains a beta2 directory with PolyFun outputs for each traits (used in the omnigenicity analyses) #gwas_catalog_cS2G.zip<br> This 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)<br> PUBMEDID: PUBMED ID<br> DISEASE.TRAIT: PHENOTYPE<br> CHR: Chromosome<br> POS: Position (hg19)<br> SNP: SNP ID<br> GENE: Gene ID<br> cS2G: cS2G score<br> INFO: S2G scores for the 10 main functional S2G (including the 7 cS2G constituent strategies) #pergeneh2_cS2G_UKBB.zip<br> This compressed file contains per gene heritability for 19,995 genes in 49 UK Biobank traits<br> GENE: name of the gene<br> h2gene: heritability linked to genes using cS2G<br> Mgene: sum of the linking scores for SNPs with a beta2&gt;0<br> h2gene_common: heritability of common SNPs linked to genes using cS2G<br> Mgene_common: sum of the linking scores for common SNPs with a beta2&gt;0<br> h2gene_lowfreq: heritability of low-frequency SNPs linked to genes using cS2G<br> Mgene_lowfreq: sum of the linking scores for low-frequency SNPs with a beta2&gt;0 #S2G_original.zip<br> This compressed file contains original S2G startegies that we computed (fine-mapped eQTLs), obtained through personal coomunication (Cicero), or accessed online. #sumstats_63.zip<br> This compressed file contains the 63 independent summary statistics, and additional blood/immune traits #sumstats_UKBB122K.zip<br> This compressed file contains the 49 UK BiobanK summary statistics computed on N=122K and used in the omnigenicity analyses