Histone Acetylation QTL (haQTL) Resources#

Histone acetylation quantitative trait loci (haQTL) identify genetic variants that influence levels of H3K9 acetylation, an active histone mark associated with promoter and enhancer activity. This resource provides haQTL summary statistics, fine-mapping results, and colocalization analyses linking active regulatory elements to genetic variation in Alzheimer’s disease brain tissue.

Overview#

haQTL mapping was performed on H3K9ac ChIP-seq data from brain tissue using the FunGen-xQTL pipeline. Peak-level H3K9ac read counts were normalized and adjusted for covariates before tensorQTL-based association testing. Fine-mapping was performed using SuSiE-RSS. Pairwise colocalization with AD GWAS fine-mapping uses a novel epigenetic fine-mapping approach developed to map chromatin-level mechanisms of AD risk variants.

Available Datasets#

Brain Tissue#

Analyses Performed#

Single-Context Fine-Mapping#

Fine-mapping using SuSiE-RSS per H3K9ac peak, providing:

• Posterior inclusion probabilities (PIPs)
• 95% credible sets
• Effect sizes on H3K9ac signal

AD GWAS Colocalization#

Bulk haQTL–AD GWAS pairwise colocalization uses the epigenetic fine-mapping approach to identify histone acetylation-level mechanisms of AD genetic risk. Results available at syn69865816 and syn69670630.

Multi-Context Colocalization#

ColocBoost colocalization identifying shared signals between haQTL and other molecular QTL datasets is available at syn69670597.

Data Access#