Pretend for a second it's a nutrition study and apply your usual scepticism :-) You know quite well that "just run a regression" is, um... rarely that simple.

No, that's the great thing about genetic associations! First, genes don't change over a lifetime, so every association is in effect a longitudinal study where the arrow of time immediately rules out A<-B or reverse causation in which IQ somehow causes particular variants to be overrepresented; that takes out one of the three causal pathways. Then you're left with confounding - but there's almost no way for a third variable to pick out people with particular alleles and grant them higher intelligence, no greenbeard effect, and population differences are dealt with by using relatively homogenous samples & controlling for principal components - so you don't have to worry much about A<-C->B. So all you're left with is A->B.

To give one obvious example, interaction effects are an issue, including interaction between genes and the environment.

But they're not. They're not a large part of what's going on. And they don't affect the associations you find through a straight analysis looking for additive effects.