Cis-eQTL summary statistics across GENCODE annotations and quantification methods from GTEx v8

This dataset contains nominal cis-eQTL summary statistics from QTLtools (v1.3.1) applied to GTEx v8 short-read RNA-seq data across 48 tissues. Results are provided for three GENCODE annotation versions (v27, v38, and v45) and two quantification methods (Salmon and STAR+featureCounts). For each tissue-annotation-method combination, the dataset includes nominal association results for all cis-SNPs within 1 Mb of each tested gene with gene expression rank-normalized prior to QTL mapping. These data accompany the manuscript "Quantification method affects replicability of eQTL analysis, colocalization, and TWAS" (Head et al., biorXiv 2025), which provides detail on statistical methods and demonstrates that quantification method and transcriptomic annotation choice substantially affect eGene detection, expression prediction, colocalization, and TWAS results. Files: Summary statistics are organized by tissue, and each tissue folder contains nominal QTL results for each annotation-quantification method combination. Columns: Each gzipped .txt file has the following column format: 1 phe_id The gene ID (phenotype ID) 2 phe_chr The phenotype chromosome 3 phe_from Start position of the phenotype 4 phe_to End position of the phenotype 5 phe_strd The phenotype strand 6 n_var_in_cis The number variants in the cis window for this phenotype. 7 dist_phe_var The distance between the variant and the phenotype start positions. 8 var_id The variant ID. 9 var_chr The variant chromosome. 10 var_from The start position of the variant. 11 var_to The end position of the variant. 12 nom_pval The nominal p-value of the association between the variant and the phenotype. 13 r_squared The r squared of the linear regression. 14 slope The beta (slope) of the linear regression. 15 best_hit Whether this varint was the best hit for this phenotype.