How does rectal cancer differ from colon cancer?
The type of tissue is different.
Cancer cells need to have different features to reside in different types of tissue.
The features unique to cancer cells resident in each type of tissue are termed as 'markers', and these features can be used to identify or even target these cells.
To illustrate this concept, let's say a specific mutation in a specific gene of a cancer cell makes it such that the cell is more 'at home' in the rectum than the colon. This mutation would be a marker of rectal cancer, and not colon cancer.
A literature search should give you lists of markers that distinguish between the two types of cancers.