As for where the alleles come from, human reproduction and DNA replication is an error prone process. Genetic variation always arises from an expanding population.
No matter which way you slice it, all the different alleles could not have been present in two human beings (maximum allelic variety of four), and it is mathematically impossible that all those alleles were present in the original human population.
Allelic variety increases with time in an expanding population. This has been seen in numerous observations and it comports well with what we see in humans.
From an original population humans have spread out over the globe and differentiated based upon differing environmental needs.
And if DNA reproduction (and its subsequent mixing in a small population) produces changes, even beneficial ones, might not this be the source of genetic novelty?
The vitamin D question is an interesting one. Are you suggesting vitamin D levels are related to degrees of skin pigmentation?