ok, Chromosomes are something you brought up. Saying something is genetic does not mean i was talking about Chromosomes, but i think that is just a misunderstanding between us in the use of that word.
A Chromosomes is a package of dna (between ~16 mm long and 85 mm long, but not stretched out like that, it is packaged up rather tightly, and the chromosome is the name of the package)
What you want to talk about is probably genes. Specific sections of DNA which code for proteins, which do the general work of every bodily function... and NO i can't tell you which gene is involved, though it is likely that there are several genes which work (along with other 'junk DNA' which regulate, but don't code directly) to map out the development of gender identity (and the structures in the brain which are setup for this.)
But you're entirely wrong in saying that i can't speak for the certainty.
We are very lucky to have experiments which involving twins to do just that. Identical twins raised apart give us the ability to contrast the different impact environment and genetic components have on development.
Likewise it is possible to compare identical twins, non-identical twins and siblings (who are genetically as similar as non-identical twins, but didn't share the same womb at the same time, which is considered an 'environmental' effect) - this lets you look at the percentage of siblings where one is trans-gendered, and then see how likely it is that a brother or sister will be. Contrasted with that chance for non-identical twins, and identical twins, gives us a rather decent idea which factors have the largest impact.
And as this is a statistical analysis, it is only a limited estimate, but with enough candidates you can get a decent percentage.