ROSMAP meQTL Results for Endothelial cells with CpGs

This dataset contains methylation quantitative trait loci (meQTL) results for the following study:

"regionalpcs improve discovery of DNA methylation associations with complex traits"

Tiffany Eulalio*¹, Min Woo Sun¹, Olivier Gevaert¹, Michael D. Greicius², Thomas J. Montine³, Daniel Nachun*‡³, Stephen B. Montgomery*‡^1,3

‡ These authors contributed equally as senior authors

* Corresponding authors: Tiffany Eulalio (eulalio@alumn.stanford.edu), Daniel Nachun (dnachun@stanford.edu), Stephen B. Montgomery (smontgom@stanford.edu)

 Author affiliations:

1.     Department of Biomedical Data Science, Stanford University, Stanford, CA

2.     Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA

3.     Department of Pathology, Stanford University, Stanford, CA

Dataset description:

This dataset contains QTL results generated from FastQTL, organized by region type (full gene, gene body, preTSS, and promoters) and summary types (averages and regional principal components).

Contents:

• Parquet tar files: These compressed archives contain output files in Parquet format from FastQTL, split by chromosome. parquet1 includes chromosomes 1-10, and parquet2 includes chromosomes 11-22.
• cis_qtl_summary_stats.csv: Provides summary statistics for each phenotype-variant pair, including effect sizes, p-values, TSS distances, and additional details.
• cis_qtl.signif_pairs.csv: Contains the significant QTL results identified by FastQTL.
• cis_qtls.time_to_run.txt: Reports the running time for FastQTL analysis.
• cis_qtls.cis_qtl.txt.gz: Contains comprehensive results for all cis QTLs.

This dataset is intended to support replication and further exploration of QTL associations across different genomic regions and summary methods.