To cite HapMap in publications use:

  The International HapMap Consortium. The International HapMap
  Project. Nature 426, 789-796 (2003).

A BibTeX entry for LaTeX users is

  @Article{,
    title = {The International HapMap Project},
    author = {The HapMap Consortium},
    year = {2003},
    url = {http://www.nature.com/nature/journal/v426/n6968/abs/nature02168.html},
    journal = {Nature},
    pages = {789--796},
    volume = {426},
  }

The HapMap Consortium invested lots of effort in generating these data.
Please cite it.