There is an interesting study I read recently on this very topic. It was on the fur color of mice. The study basically indicates that developmental factors may change methylation of the DNA in a way to change the anticipated phenotype. The study of these types of factors which are not directly related to the genetic code but may effect regulation of gene expression is referred to as epigenetic. Methylation is one major epigenetic factor. Other major epigenetic factors include the packaging of the DNA and histone modifications along with several more. The theory is that modifications to the DNA allow or disallow access of transcriptional machinery, (i.e. the RNA polymerase complex.) This thereby changes the transcription profile and the protein profile downstream. This can have effects on phenotype if these changes effect developmental protein production.