Thanks! By the way, when you say "you can download the human genome", presumably this is the genome of a specific individual whose DNA was sequenced? What person is that?
genomic regions with higher variability between individuals are annotated separately and are not represented in the main chromosomal sequence, but can be aligned to it as such.
http://hgdownload.soe.ucsc.edu/goldenPath/venter1/bigZips/
However, the human "reference" genome (the updated main product of the Human Genome Project) is a patchwork of about 20 donors' genomes. Many(most?) of the donors are anonymous volunteers from Buffalo, NY, USA.