I would expect it's not caused by genes themselves, but by control DNA. That's where a lot of the subtle structural stuff happens. But that's also hard to test for. It's like how you can't test how tall someone is going to be.

I've also read ages ago in Scientific American that the difference between our brains and chimp brains is almost entirely in control DNA, not in genes. It matters a lot, but is often overlooked. (It used to be called "junk DNA", before people realised how important it was.)