Abstract Introduction Genome-wide association study (GWAS) is a powerful method to study disease mechanisms but significant challenges exist. Most GWAS results reside in non-coding genomic regions and methods that derive mechanisms from genetic signals, such as expression quantitative trait locus analysis, fail to incorporate relevant exposures. We introduce chromatin accessibility quantitative trait locus (ca-qtl) analysis, which uses read-specific data from the assay for transposase accessible chromatin with sequencing (ATAC-seq) to determine allelic imbalance in cell-type- and exposure-dependent-conditions. Methods We applied a genome-wide ca-qtl analysis using ATAC-seq reads in cultured and primary airway epithelial cells from 15 donors (total libraries = 48) by counting allele-specific reads at common single nucleotide variants (SNVs, minor allele frequency 0.01) coded in dbSNP156. Only obligate heterozygote SNVs (minimum two alleles in each library) with reads in 3 or more libraries were included (n = 69,203 SNVs). The population frequency for each SNV was obtained from dbGaP. We then analyzed 52 candidate SNVs identified in a modified GWAS Gupta et al 2025 using an additional 44 ATAC-seq libraries from 5 donors that were exposed in culture to air pollution-relevant exposures. We defined significant ca-qtls that fell outside of a 95% genome-wide prediction interval or applied a ranked z-score method to define significant delta-ca-qtls, which change allele frequency between unstimulated and exposed samples. Results Three of 52 ca-qtls (rs3861144, rs11883931, and rs162481) fell outside the 95% genome-wide prediction interval, including two delta-ca-qtls (rs11883931 and rs162481) with significant allele frequency changes with exposure. rs3861144 and rs11883931 were previously associated with asthma risk and lung function in two independent cohorts and reside in exposure-dependent transcriptional regulatory elements in airway epithelial cells. We investigated rs3861144 in detail and identified a pathway where SPRY2 is involved in asthma risk by regulating monolayer repair and cytokine secretion in airway epithelia following particulate exposure Gupta et al 2025. rs11883931 was previously found in a differentially-methylated region in airway epithelial cells from patients with COPD Morrow et al. 2016. Conclusions Ca-qtl analysis prioritizes non-coding GWAS results for functional significance with tissue and exposure specificity. In this pilot experiment, we demonstrated that most SNVs are not significant ca-qtls, and the allele frequency in ATAC-seq reads follows the allele frequency in the population. However, SNVs with significant ca-qtls have important transcriptional and epigenetic functions, as demonstrated by rs3861144 and rs11883931. Future application of this method will advance genetic study by identifying tissue- and exposure-specific disease mechanisms. This abstract is funded by: NIH
Gupta et al. (Fri,) studied this question.