A polymorphism is a variation in DNA sequence that is common in the population.
A Single Nucleotide Polymorphism [SNP] occurs when one single base is replaced by another. There are millions of SNPs in the human genome.
No single allele is regarded as the standard sequence. What we have are two or more equally acceptable alternatives [alleles].
The 1% cut off point
There is an arbitrary cut-off point that distinguishes a mutation from a polymorphism and this is regarded as greater than or equal to a 1 per cent prevalence in a population. In other words for a genetic change to be classed as a polymorphism, the least common allele must have a frequency of 1per cent or more in the general population.
If the frequency in a population is found to be lower than 1%, the allele is then regarded as a mutation.
Most SNPs occur in non-coding regions of DNA i.e. in the 'Junk DNA' regions but may also occur in coding [gene] areas of DNA and can thus influence a particular protein such as an enzyme or a signalling molecule or a receptor etc.
Protein function is dependend on the three dimensional [3D] structure of the protein molecule. This is determined by the amino acids that make up the protein. The structure of an amino acid is shown below.
Some amino acids are hydrophilic [water-loving] some are hydrophobic [water-hating] and others are ambivalent [can swing either way]. The SNP tutorial at the bottom of this page describes this aspect of protein folding and function. An error [SNP] that places a particulr amino acid in the wrong place say a hydrophobic amino acid where a hydrophilic amino acid should be, may cause disastrous effects on protein folding and thus protein function. Remember proteins could be receptors, signaling molecules, hormones, structural components etc.
SNPs and Chronic Diseases
Even subtle effects of a SNP can influence the susceptibility of developing common illnesses such as heart disease, hypertension, Alzheimer's disease, diabetes etc.
Mendelian mutations such as Cystic Fibrosis or Muscular Dystrophy make up a very small part of the genetic mutation spectrum and such mutations could not provide an answer to all the chronic diseases that afflict humanity. SNPs have been the 'holy grail' for geneticists and are showing distinct links between certain SNPs and chronic illnesses such as hypertension, diabetes, the metabolic syndrome, heart disease etc. that could never be explained by a '1 gene = 1 disease' model before the discovery of SNPs. For medicine this is an amazing breakthrough and promises to move humanity towards a bright and promising new paradigm in clinical treatment and this is termed 'Personalized Medicine'. The year 2007 was marked as the annus mirabilis [the miracle year] of genomics. The other exceptional annus mirabilis of science was when Einstein published his theory of relativity and a golden era of physics unfolded, the benefits of which surround our daily lives today. What medical marvels await humanity in this golden age of genomics.
There are millions of SNPs and only a handful have been discovered. The complexity lies in the fact that a particular SNP may or may not be significant and needs to be placed in the context of the individual and their environment and lifestyle. A good example is the CYP1A1 mutation that could either be an advantage or a disadvantage in a particular individual. CYP1A1 has the potential to shift estrogen metabolism to the weak and beneficial 2-hydroxy [2OH] form of estrogen. However, CYP1A1 also has the potential to convert compounds such as heterocyclic amines from charred meat or compounds found in cigarette smoke into highly carcinogenic compounds. So in this circumstance CYP1A1 in a female non-smoker could be of great benefit but could be a double-edged sword in a smoker.
It is important to note that because you have a SNP, it doesn't mean that you will develop a disease or a characteristic [phenotype]. It is simply a probability game.