Human genetic diversity in Africa in comparison with the rest of the world
Here is a tree based on mitochondrial DNA variations in human populations.

van Oven M, Kayser M.  Hum Mutat. 2009 Feb;30(2):E386-94. 
Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation.



Looking at genetic distance between populations via mitochondria DNA, all nonafricans are descended from a founder in one mtDNA group (L3).  All the other L groups are African populations: L0 is the San people, L1 is Mbenga pygmies, L5 is Mbuti pygmies, and the others are other African groups.  

If one considers each L haplogroup to represent genetic variation then 5/6 (83%) of human genetic variation is from African populations.

From a different source looking at genetics differently   A map of human genome variation from population scale sequencing Nature. 2010 Oct 28; 467(7319): 1061–1073


  Populations with African ancestry contributed the largest number of
  variants and contained the highest fraction of novel variants,
  reflecting the greater diversity in African populations. For example,
  63% of novel SNPs in the low coverage project and 76% in the exon
  project were discovered in the African populations, compared to 20%
  and 33% in the European ancestry populations for the exon and low
  coverage projects respectively.