Hereditary Transthyretin (TTR) Amyloidosis (hATTR) is a rare life-threatening disorder caused by amyloidogenic coding mutations located in TTR gene. To understand the high phenotypic variability observed among carriers of TTR disease-causing mutations, we conducted an epigenome-wide association study (EWAS) assessing more than 700,000 methylation sites and testing i) TTR coding mutation carriers vs. non-carriers, and ii) Val30Met (rs28933979) carriers vs. carriers of other TTR mutations. In the first analysis, we observed a significant methylation change at cg09097335 site located in Beta-secretase 2 (BACE2) gene (beta =-0.60, p=6.26x10-8). This gene is involved in a protein interaction network enriched for biological processes and molecular pathways related to amyloid-beta metabolism (Gene Ontology:0050435, q=0.007), amyloid fiber formation (Reactome HSA-977225, q=0.008), and Alzheimers disease (KEGG hsa05010, q=2.2x10-4). Additionally, TTR and BACE2 share APP (Amyloid-beta precursor protein) as a validated protein interactor. In the second analysis, we observed that Val30Met carriers have a significant hypomethylation at cg13139646 site located in TTR exonic region (beta=-2.18, p=3.34x10-11). A methylation quantitative trait locus analysis considering a 20 Kb region including TTR coding and non-coding regions suggested that TTR coding variants (Ile68Leu, rs121918085; Ala120Ser, rs876658108; Gly6Ser, rs1800458) have independent effects on cg13139646 methylation, while no independent effect was observed for non-coding variants. In conclusion, we provide novel insights related to the molecular mechanisms involved in the complex heterogeneity of hATTR, highlighting the role of epigenetic regulation in this rare disorder.