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There are lots of YC companies who have hired foreigners, and have paid for the H1B, T1N, etc. (I'm basing this on the YC mailing list traffic). It seems to happen frequently.

I'm not sure off-hand which ones are open to this, but my guess is for a good engineer plenty are (particularly the larger ones). We'll try to find out for you.

I think you should submit. For a great hire, a great start-up will pull out the stops and help you sort out an appropriate visa.