Characterization of caffeine response regulatory variants in vascular endothelial cells

Output from DESeq2. Column ‘V1’ is the genomic position (hg19) of the SNP within the construct being tested, ‘baseMean’ refers to normalized expression, ‘log2FoldChange’ refers to the effect size, ‘lfcSE’ is the standard error of the effect size, ‘stat’ is the log2FoldChange divided by lfcSE, ‘pvalue’ is the nominal p-value, and ‘padj’ is the adjusted p-value. Please refer to DESeq2 documentation for additional details.

Includes all variants in the designed library that are within a motif from the JASPAR 2022 CORE Vertebrates database determined by PWMScan. Columns 1–3 are the genomic position of the test SNP, column 4 is the rsID for the test SNP, and column 5 is the ID of the motif in JASPAR.

Includes contingency tables for all Fisher’s exact tests reported in this study. Please see the legend provided within the file. Briefly, A1–C5 is the contingency table and summary of results for ASE variants within open chromatin regions, A6–C10 for ASE variants overlapping with artery eQTLs, A11–C15 for cASE variants within open chromatin, and A16–C20 for cASE variants overlapping with artery eQTLs.

Output from ASE/cASE analysis. The ‘identifier’ column is the SNP/direction pair, ‘meta_estimate’ is the effect size (of the ASE), ‘meta_se’ is the standard error of the effect size, ‘n’ is the number of replicates containing nonzero read counts, ‘DNA_prop’ is the proportion of reads (reference/alternate) present in the DNA library, ‘meta_z’ is the z-score, ‘meta_p’ is the nominal ASE p-value, ‘meta_padj’ is the adjusted ASE p-value before filtering for SNP/direction pairs where n > 3, ‘new_padj’ is the adjusted ASE p-value after filtering for SNP/direction pairs where n > 3, ‘group’ refers to the applicable condition for the statistic (.x suffix for caffeine, .y suffix for control), ‘case_z’ is Z_T-Z_C, ‘case_p’ is the nominal p-value for cASE, and ‘case_padj’ is the adjusted p-value for cASE.

The ‘chr’ column contains the chromosome information, ‘pos’ is the genomic position (0-based, hg19), ‘pos1’ is the genomic position (1-based, hg19), ‘identifier’ is the SNP/direction pair, ‘rsID’ refers to rsID, ‘padj_min’ refers to the minimum p-adjusted value for ASE (across conditions), ‘ID’ is an ID to identify the genomic position in the format of chr_pos1, ‘PIP’ is the posterior inclusion probability as calculated by DAP-G, ‘gene’ refers to the Ensembl gene ID, ‘tissue’ refers to the GTEx artery tissues (tibial, aorta, or coronary), ‘group’ identifies if the variant has significant ASE or significant cASE, ‘case_p’ refers to the cASE nominal p-value, and ‘case_padj’ refers to the cASE adjusted p-value.

The ‘Identifier’ column is the SNP/direction pair, ‘ID’ is an ID to identify the genomic position in the format of chr_pos1 (see above), ‘Gene ID’ refers to the Ensembl gene ID, ‘Gene symbol’ refers to the gene symbol, ‘Trait’ is CAD or hypertension (HTN), ‘Tissue’ refers to the GTEx artery tissues (tibial, aorta, or coronary), ‘DAP-G PIP’ is the posterior inclusion probability as calculated by DAP-G, ‘GWAS z-score’ is the z-score for the GWAS of the corresponding trait, ‘GWAS pvalue’ is the nominal p-value for the GWAS of the corresponding trait, ‘PTWAS-INTACT PCG’ is the probability of being a putative causal gene as calculated by INTACT, ‘PTWAS-INTACT FDR’ is the FDR statistic as calculated by INTACT, ‘INTACT z-score’ is the z-score statistic as calculated by INTACT, ‘cASE_p’ is the cASE nominal p-value, ‘cASE_padj_(original)’ is the cASE adjusted p-value, ‘cASE_z’ is Z_T-Z_C, ‘DE_construct?’ indicates if the construct is significantly differentially active as defined by our assay, ‘Caffeine_ASE_z’ is the z-score for ASE (caffeine condition), ‘Water_ASE_z’ is the z-score for ASE (control condition), ‘centiSNP motifs’ refers to motifs the SNP is within as identified by centiSNP, and ‘centiSNP category’ refers to if the motif is a footprintSNP, effectSNP, or switchSNP as identified by centiSNP.

Read counts for all libraries at different steps of the data processing pipeline. ‘Library Name’ is an identifier used for the sample, ‘Treatment’ is the condition (caffeine or control), ‘Dedup’ refers to the number of reads after deduplication, and ‘>1 read either direction’ describes the number of reads that have >1 read for each allele in either direction.