**Where can I download the population frequency data of all mitochondrial variants?**

I checked [the HapMap database][1], but it only includes the nuclear variants.

 [1]: http://hapmap.ncbi.nlm.nih.gov/downloads/frequencies/latest_phaseII_ncbi_b36/fwd_strand/non-redundant/
The GenBank frequency data (out of about 30k full length mitochondrial sequences) for any given variant is available in [MITOMASTER][1]

MITOMAP provides curated polymorphisms and disease dumps of various formats with these counts and frequencies

 - http://mitomap.org/cgi-bin/disease.cgi?format=vcf
 - http://mitomap.org/cgi-bin/polymorphisms.cgi?format=vcf

These will probably evolve as we develop breakdowns by major haplogroup.

 [1]: http://mitomaster.mitomap.org