  Single nucleotide polymorphisms (SNPs) represent an important type of dynamic
sites within the human genome. These common variants often locally correlate
into more complex multi-SNP haploblocks that are maintained throughout
generations in a stable population. The information encoded in the structure of
common SNPs and SNP haploblock variation can be characterized through a
normalized information content (NIC) metric. Such an intrinsic measure allows
disparate regions of individual genomes and the genomes of various populations
to be quantitatively compared in a meaningful way.
  Using our defined measures of genomic information, the interplay of
maintained statistical variations due to the environmental baths within which
stable populations exist can be interrogated. We develop the analogous
"thermodynamics" characterizing the state variables for genomic populations
that are stable under stochastic environmental stresses. Since living systems
have not been found to develop in the absence of environmental influences, we
focus on describing the analogous genomic free energy measures in this
development.
  The intensive parameter describing how an environment drives genomic
diversity is found to depend inversely upon the NIC of the genome of a stable
population within that environment. Once this environmental potential has been
determined from the whole genome of a population, additive state variables can
be directly related to the probabilities of the occurrence of given viable SNP
based units (alleles) within that genome. This formulation allows the
determination of both population averaged state variables as well as the
genomic energies of individual alleles and their combinations. The
determination of individual allelic potentials then should allow the
parameterization of specific environmental influences upon shared alleles
across populations in varying environments.
