Vannakkam: Genetic studies like this one ...
http://www.cousincouples.com/?page=overview have largely dispelled the myth that bad things happen in cousin marriage. Yes, the risk is slightly higher, but decreases the further you get away, and in your case it's second cousin, not first. The risk also increases when the behaviour is repeated in a particular community over a long period of time, like over many generations. This happened in certain caste based smaller groups or small pockets of people, like on islands like Pitcairn.
For some reason, some elements in the west have attached a stigma to it, and the myth has grown over time, with little or no scientific evidence to go back it up.
So knowing this, I'd say just go ahead and marry the girl of your dreams. I personally know several first cousin marriages in the Hindu community, and I'm not aware of any genetic factors being present, but observational anecdotes aren't true science.
You can do your own research on line as well.
Aum Namasivaya
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