The human genotope is the convex hull of all allele frequency vectors that
can be obtained from the genotypes present in the human population. In this
paper we take a few initial steps towards a description of this object, which
may be fundamental for future population based genetics studies. Here we use
data from the HapMap Project, restricted to two ENCODE regions, to study a
subpolytope of the human genotope. We study three different approaches for
obtaining informative low-dimensional projections of this subpolytope. The
projections are specified by projection onto few tag SNPs, principal component
analysis, and archetypal analysis. We describe the application of our geometric
approach to identifying structure in populations based on single nucleotide
polymorphisms
