Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits: Summary Statistics

Summary statistics for the QTL analyses present in "Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits" published in 2020 in AJHG. Data includes multiple treatments listed within the file names. eQTL data was produced by taking rpkm normalized expression data (RNA-seq) or log normalized expression data (Microarray), and running these through matrixeQTL correcting for the top 4 PCs from a PCA on he genotypes (to correct for ancestry), genetic sex, and 15 factors (RNA-seq) or 30 factors (Microarray) from PEER. FDRs were calculated per each phenotype, so each SNP had its pvalue adjusted via Benjamini-Hochberg correction for all other SNPs tested for that transcript's expression. Columns provided:SNP - rsID of the SNP (some may also list position and alleles following a ":")Gene - Refseq ID of the gene tested [aka. NM_XXXXX]Ref - the reference allele for this SNP in our studyAlt - the alternate allele for this SNP in our studyCrude.pvalue - The pvalue with no correctionFDR - the gene-level corrected pvalue as described aboveBeta - the beta of the association (- means ref is higher expression) molQTL data was produced by taking rpkm normalized data, as well as allele specific counts for ATAC-seq (chromatin accessibility) and ChIP-seq (ERG binding, p65 binding, H3K27ac) and running them through the program RASQUAL. The Q-values were produced by RASQUAL on a per peak basis, meaning SNPs were corrected for all the other SNPs tested against the reads from a single peak. Columns provided:SNP - rsID of the SNP (some may also list position and alleles following a ":")Chrom -The chromosome the peak and SNP are locatedStartPeak - The starting position of the peak in hg19EndPeak - The end position of the peak in hg19 Ref - the reference allele for this SNP in our studyAlt - the alternate allele for this SNP in our studyQ-value - the peak-level corrected p-value as described aboveASR - the allele specific ratio of the association (less than 0.5 mean the ref has higher reads, greater than .5 means the alt has higher reads [all within Heterozygous individuals])