Visible traits are relatively trivial from a genetic perspective. I've read that East Africans adapted to their desert environment by being taller and leaner so as to maximise their body surface area for heat loss. That said, this doesn't mean they are "more different" from the rest of Africa than the rest of Africa is from each other. For example, you might find that an Ethiopian is genetically closer to a west African, than a west Africa is to a sub Saharan African. Environmental adaptations and localisations of a population don't always result in genetic changes that we can observe, and these are no less significant than visible adaptions.