Cousin Marriage from genetics point of view
The problem is that humans have 22 other pairs of chromosomes than just the sex chromosomes X and Y. Reproducing with your cousin (the son of your mother's brother is the son of your uncle which means your cousin) is generally looked down upon because of inbreeding. 

Here's how it breaks down. Your mother and her brother (your uncle) each received 50% of their genes from your grandmother, and 50% from your grandfather. You received 50% of your genes from your mother and the other 50% from your father, who presumably is unrelated to the family. Therefore, you received 25% (50% of 50%) of your genes from your grandmother, and 25% from your grandfather. The same is true of your cousin - 25% from grandmother, and 25% from grandfather. The chances of some of your 25% and his 25% overlapping are rather high (for any one allele of a gene, it has a 1 in 4 chance of being the same as the cousin's). Combine that with 19-20,000-something genes, and that's a lot of overlap.

The problem with overlap/inbreeding is that any "hidden" (recessive) alleles may become homozygous. This may not be a problem for some genes, but a rather big problem for others (see my previous answer about Hunter Syndrome for an example.) There is a real potential of serious genetic diseases in any children resulting from such a relationship, which of course isn't fair to them.