Single-molecule Fiber-seq analysis with the FIRE computational framework enables comprehensive haplotype-resolved mapping of chromatin accessibility across the 6 Gbp diploid human genome, revealing that haplotype-selective chromatin accessibility arises from three distinct mechanisms: genetic variants that disrupt regulatory elements and drive disease associations (particularly concentrated in the HLA locus), parent-of-origin imprinting that can occur independently of CpG methylation, and mitotically stable somatic epimutations that create non-deterministic chromatin patterns propagated through clonal expansion.

Diploid human cells contain two non-identical genomes, and differences in their regulation underlie human development and disease. We present Fiber-seq Inferred Regulatory Elements (FIRE) and show that FIRE provides a more comprehensive and quantitative snapshot of the accessible chromatin landscape across the 6 Gbp diploid human genome, overcoming previously known and unknown biases afflicting our existing regulatory element catalog. FIRE provides a comprehensive genome-wide map of haplotype-selective chromatin accessibility (HSCA), exposing novel imprinted elements that lack underlying parent-of-origin CpG methylation differences, common and rare genetic variants that disrupt gene regulatory patterns, gene regulatory modules that enable genes to escape X chromosome inactivation, and autosomal mitotically stable somatic epimutations. We find that the human leukocyte antigen (HLA) locus harbors the most HSCA in immune cells, and we resolve the specific transcription factor (TF) binding events disrupted by disease-associated variants within the HLA locus. Finally, we demonstrate that the regulatory landscape of a cell is littered with autosomal somatic epimutations that are propagated by clonal expansions to create mitotically stable and non-genetically deterministic chromatin alterations.