Downloads

All COPs in GTEx

File containing all COPs identified across GTEx tissues and displayed in the database, includes both positively and negatively correlated COPs. Only significant cases (FDR 1%) are included.

• gene1_id → ensembl (ENSG) ID of the first gene
• gene1_name → HUGO gene name of the first gene
• gene2_id → ensembl (ENSG) ID of the second gene
• gene2_name→ ensembl (ENSG) ID of the second gene
• tissue → GTEx tissue in which the COP was identified
• correlation → Pearson correlation between the gene pair expression across individuals
• tss_distance → absolute distance between the transcription start sites (TSS) of the genes in the pair
• p_value → empirical p-value calculated for the observed (absolute) correlation to be higher than expected by chance through permutation of expression values

all_cops_gtex.tsv

All COPs in GTEx used for publication

filtered_cops_gtex.tsv

All lead eQTLs in GTEx

File containing all lead eQTLs across GTEx tissues. Only significant cases (FDR 5%) are included. Coordinates are in GRCh38.

• rs_id → rsID of the variant
• variant_id → coordinate and alleles of the variant (from GTEx)
• slope → slope of the regression
• nominal_p_val →  nominal P-value of association between the phenotype (gene) and the variant
• adjusted_p_val →  QTLtools [see https://qtltools.github.io/qtltools/] permute P-value of association adjusted for the number of variants tested in cis given by the fitted beta distribution
• fdr_0.05 → FDR-adjusted P-value (Benjamini-Hochberg procedure at 5% FDR)
• gene_id → ID of gene/phenotype (ENSG) in association test
• gene_chr → chromosome ID of the phenotype
• gene_tss → transcription start site (TSS) of the phenotype
• gene_strand → strand of the phenotype
• n_variants → total number of variants tested in cis
• distance_tss → distance between the gene TSS and the variant
• tissue → GTEx tissue in which the associate test was performed

all_lead_eqtls_gtex.tsv

All shared eQTLs in GTEx

File containing all shared eQTLs across GTEx tissues. Each row contains an eQTL which is the lead eQTL for gene1 (passing FDR 5% threshold) and also is associated with gene2 with nominal P-value < 0.05. Coordinates are in GRCh38.

• rs_id → rsID of the variant
• variant_id → coordinate and alleles of the variant (from GTEx)
• gene1_lead → Gene for which the variant is the lead eQTL
• gene1_lead_permutation_pval → FDR-adjusted QTLtools [see https://qtltools.github.io/qtltools/] permute P-value of association adjusted for the number of variants tested in cis given by the fitted beta distribution, for gene1_lead
• gene2_other → other gene in the COP which is also associated to this variant
• gene2_other_nominal_pval → nominal P-value of association between the phenotype (gene) and the variant (not FDR corrected)
• tissue → GTEx tissue in which the associate tests were performed 

shared_eqtls_gtex.tsv

All COPs and eQTLs in Geuvadis LCLs

geuvadis_lcl.tgz

Single cell iPSC COPs

cuomo2021_sc_cops.tsv

Single cell LCL COPs

shareseq_sc_cops.tsv