Lactose intolerance, technically known as hypolactasia, is frequent in many populations. Lactase is the enzyme that digests the lactose in milk, and while there is plenty of it around in mammalian infants, including most humans, lactase activity generally declines after weaning. In some individuals, though, lactase activity persists at a high level throughout adult life, enabling them to digest lactose as adults. This dominantly inherited genetic trait is known as lactase persistence; the more evolutionarily "normal" lowered level of lactase can lead to the inability to digest lactose as an adult and thus lactose (and milk) intolerance.
Lactose intolerance typically increases with age, and a reasonable percentage of individuals with symptoms of irritable bowel syndrome may actually be lactose intolerant. Note that different populations differ in the SNP associated with hypolactasia, and not all SNPs associated with lactose intolerance have been discovered (yet). Wikipedia
Lactose intolerance has primarily been linked to SNPs found in the introns of the MCM6 gene which turn out to have some control over the lactase LCT gene located many thousands of base pairs away. These SNPs include:
- rs4988235 and rs182549, for which the (T) and (A) alleles, respectively, form a haplotype predicting lactase persistence (thus avoiding lactose intolerance) in 77% of Europeans studied. [PMID 11788828, PMID 15114531]
- A different SNP, rs145946881, known as "G/C-14010", appears to be associated with lactase persistence in sub-Saharan African populations. Two other nearby SNPs, rs41380347 "T/G(-13915)" and rs41525747 "C/G(-13907)", are also associated to a lesser degree. [PMID 17159977, PMID 23029545]
wikipedia:Image:LacIntol-World2.png world map of lactose intolerance
This 2012 article is a reasonably comprehensive review of the genetics of lactase persistence.