That is very strange. It does look to be a brown pigmented spot on her cornea. This is why it is "see through" because the cornea is see-through.
When ulcers heal or scar over, they often don't get pigment that just "appears". They will just simply be grey or white-ish in color, that is an opacity in the cornea, because it is a scar.
I do not believe it is a uveal cyst, because I think this is on the cornea. The uvea is a collective term that is made up of three structures: The iris, the ciliary body, and the choroid. Obviously, the iris is the colored part of the eye. The ciliary body is what holds the lens of the eye in place, and produces aqueous (the fluid located in the anterior chamber of the eye ... the space between the cornea and lens). And the choroid is a vascular layer that lines the entire inside of the eye. Check out the anatomy pic above to find where each of these things are.
This is a uveal cyst. Very dark in color, and certainly not see-through.
Evident in the second photo, the brownish pigment is not on the iris, and is indeed in the cornea.
Pictures can only do so much though. I'd much rather see it in person before trying to make an educated guess on what it might be. It really depends what layer of the cornea the pigment is in, although 90% of the time it is going to be on the backside of the cornea.
Melanomas are very often seen on the conjunctiva (the white part of the eye, which horses don't have very much of) but I have yet to see one happen on the cornea. The cells in the cornea are way different than any other cells in the body.
What my best guess is at this point is that her iris is rubbing on the lens behind it, which is releasing pigment from the back of the iris (all irises have brown pigment on the back of them; it's called the posterior pigmented epithelium) and then the natural circulation of the eye causes it to "stick" and stay on the backside of the cornea. In humans, this is known as pigment dispersion syndrome, which can lead to glaucoma.
But that's a total wild guess since I can't see your horse's eye for myself.
Either way, I highly doubt this is something that appeared rapidly overnight, or anything you need to rush to get the vet to see her ASAP or anything. But it should be looked at at some point.
When in doubt, have the vet out!!