The genetic basis underlying normal variation in the pigmentary traits of skin, 
hair and eye colour has been the subject of intense research directed at 
understanding the diversity seen both between and within human populations. A 
combination of approaches have been used including comparative genomics of 
candidate genes and the identification of regions of the human genome under 
positive selection, together with genome-wide and specific allele association 
studies. Independent selection for different pigmentation gene sets has been 
found between Asian, European and African populations. Several genome-wide 
association studies for pigmentation have now been conducted and identified 
single nucleotide polymorphism (SNP) markers in known, TYR, TYRP1, OCA2, 
SLC45A2, SLC24A5, MC1R, ASIP, KITLG and previously unknown SLC24A4, IRF4, TPCN2, 
candidate genes. The contribution of SNP polymorphisms present in populations 
from South Asia have been tested and alleles found at TYR, SLC45A2 and SLC24A5 
can largely account for differences between those of darkest and lightest skin 
reflectance using a simple additive model. Skin and hair colour associations in 
Europeans are found within a range of pigmentation gene alleles, whereas 
blue-brown eye colour can be explained by a single SNP proposed to regulate OCA2 
expression. Functional testing of variant alleles has begun to connect phenotype 
correlations with biological differences. Variant MC1R alleles show direct 
correlations between the biochemical signalling properties of the encoded 
receptor and the red-hair fair skin pigmentation phenotype. Direct testing of a 
range of clonal melanocyte cultures derived from donor skin tissue characterized 
for three causal SNPs within SLC45A2, SLC24A5 and OCA2 has assessed their impact 
on melanin content and tyrosinase enzyme activity. From a culmination of genetic 
and functional studies, it is apparent that a number of genes impacting 
melanosome biogenesis or the melanin biosynthetic pathway are candidates to 
explain the diversity seen in human pigmentation.