But between those variants that stick out like a sore thumb, and those common enough to be dredged up by the wide net of GWAS, there is a potential middle ground of variants that are moderately penetrant but are rare enough that they are missed by the net. There's also the possibility that there are many more-frequent variants that have such a low penetrance that GWAS can't statistically link them to a disease.
You can also find the publication of two individual genomes: an individual with West African ancestry and one of Han Chinese ancestry. Actually, these two single genomes don't tell us anything really about West Africans of Han Chinese - you'd need a much larger sample to do that. The significance of these studies lies in the technological advances they described - advances that will make it possible so that we will learn something about West Africans and Chinese by sequencing enough individuals to draw population-level conclusions.
And finally, one group reports some in-depth genotyping of over 3,000 Europeans. The question is, how much geographical detail lies in our genes? Are there differences between the French and the British? By and large, most genetic variation is shares, so to find these differences you need to look deeply enough. And the authors find that "an individual's DNA can be used to infer their geographic origin with surprising accuracy—often to within a few hundred kilometres."
That's a fairly astounding finding, no doubt due to the fact that within Europe, their are significant cultural barriers fit into a fairly small area, resulting in lots of ethnic populations.