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. <br><br>Data includes multiple treatments listed within the file names. <br><br><b>eQTL data</b> 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.<br>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)<br><br><b>molQTL data</b> 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.<br>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<br>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])