What is the difference between having anal cancer and colon cancer?

Location: An anal cancer may likely be a different cell type, located more near the skin of the anal opening. It may be treated differently with radiation and chemotherapy rather than surgery, depending on the cell type. Colon caner can be located anywhere in the large intestine, and is treated wth surgery to remove the tumor, and sometimes radiation or chemotherapy may be used after surgery.

Everything: Although both colon and anus are part of gastrointestinal tract and anus is a continuum of rectum and colon - anal cancer is completely different to colon cancer. They arise from different type of cells ( squamous vs adenocarcinoma) , they have different way of spreading, different risk factors, different therapy, prognosis etc. They are different in almost everything actually.