identifiable, polymorphic region of DNA (i.e., marker) located within a gene
(i.e., intragenic), as opposed to a flanking marker, which is located on
either side of a gene. Intragenic markers are used in linkage analysis to
track the coinheritance of the gene in question.
Definition from: GeneReviews
from the University of Washington and the National Center for Biotechnology Information
See also Understanding Medical Terminology.