Summary Statistics of eQTL analysis from a Japan clear cell renal cell carcinoma (ccRCC) cohort (n=100)

This repository details the summary statistics files generated by FastQTL (https://github.com/broadinstitute/gtex-pipeline/tree/master/qtl) for a Japan clear cell renal cell carcinoma (ccRCC) cohort (n=100), using tumor WES and paired RNA-Seq data. 1) eQTL-ccRCC-final.allpairs.txt.gz All tested cis gene-variant pairs from the nominal association test, reporting unadjusted p-values (pval_nominal), effect sizes (slope), and standard errors (slope_se). 2) eQTL-ccRCC-final.genes.txt.gz For each tested gene, the most significant cis-eQTL variant (lead eQTL), identified from the permutation-based association test (--permute 1000 10000), reporting adjusted p-values (pval_beta), effect sizes (slope), and standard errors (slope_se). qval: False discovery rate (FDR) q-value estimated across all tested genes using the qvalue method. Genes with qval < 0.05 are considered significant eGenes at 5% FDR. 3) eQTL-ccRCC-final.genes.annotated.txt.gz The same as (2), with additional gene annotation columns: gene_name (HGNC symbol) gene_chr (chromosome) gene_start (start position) gene_end (end position) strand (+ or -)