Cis-eQTL summary statistics across GENCODE annotations and quantification methods from GTEx v8
Authors/Creators
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1.
The University of Texas MD Anderson Cancer Center
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2.
University of California, Los Angeles
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3.
University of California San Diego
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4.
University of Washington
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5.
Rice University
Description
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. |
Files
Files
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