WordNet sense 1 (existing as an essential constituent or characteristic):

built-in, constitutional, integral, inbuilt, integral

WordNet sense 2 (belonging to a thing by its very nature):

intrinsic

WordNet sense 3 (in the nature of something though not readily apparent):

underlying, implicit in

WordNet sense 4 (implied though not directly expressed; inherent in the nature of something):

implicit, inexplicit