The mammalian genome within the nucleus is organized into a hierarchy of distinct chromatin folding structures and along with epigenetic modifications to the DNA influence various cellular functions such as gene expression regulation, DNA repair mechanisms, cell proliferation and differentiation. Advances in Chromosome Conformation Capture technologies have provided an ability to study the three-dimensional architecture and create high-resolution maps revealing intricate genome folding hierarchy. Despite over a decade of studies, the link between changes in chromatin folding and gene expression in post-mitotic human neurons and neurological disorders remains unclear. In this thesis, we leverage high-resolution Chromosome Conformation Capture technique (Hi-C) along with several bulk- and single-cell technologies such as RNA-seq, ChIP-seq and ATAC-seq to understand how chromatin loops are reconfigured and the role of specific epigenetic factors in modulating gene expression during human neurodevelopment, synaptic activity stimulation, and in neurological disorders. First, we show that thousands of loops are both decommissioned and gained de novo during the differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitors (NPCs) and post-mitotic neurons. We uncover that genes transitioning from RNA Polymerase II (RNAPolII) initiation to elongation phase during neural differentiation are strongly enriched for de novo cell type-specific loops and are associated with a robust increase in gene expression. Next, using human post-mitotic neurons with rare familial Alzheimer’s disease (FAD) mutations, we show genome-wide dysregulation in gene expression and mis-wiring of loops compared to isogenic wild-type (WT) neurons prior to the deposition of amyloid-beta (Aβ) plaques and phosphorylated tau tangles. We show that when genes are connected in multiple loops, the severity and direction of change in gene expression levels and single-cell burst frequency strongly correlate with the number of gained or lost promoter-enhancer loops in FAD. We find that classic architectural factors CTCF and cohesin do not change in occupancy in FAD despite genome-wide miswiring of loops. Instead, we observe that changes in RNAPolII signal correlates with loop and gene expression changes along with an enrichment for TAATTA motifs at these sites. We uncover a potential novel role for homeodomain transcription factors that have binding sites to the TAATTA motifs in genome folding and gene expression regulation. We find that the chromatin loop mis-wiring and gene expression changes is coincident with a shift in excitatory to inhibitory population in neurons carrying FAD mutations. Finally, we assess the role of chromatin loops and CTCF in the maintenance and establishment of new gene expression upon activity stimulation with potassium chloride in human neurons. We use an auxin-inducible degron system to acutely and rapidly degrade CTCF in hiPSCs derived excitatory neurons and measure the direct effect of acute CTCF loss on genome structure and gene expression. Together, this work uncovers how chromatin loops, together with epigenetics modifications, play a role in the maintenance and establishment of gene expression programs during human neural lineage commitment and in neurodegenerative disorders.