SLC45A2, SLC24A5 and MC1R - R squared: 76.3% (one SNP per gene listed)
SLC24A5, SLC45A2, ASIP - R squared: 45.7% ... interaction term of ASIP and SLC45A2 increased r-squared to 49.6% (one SNP per gene listed)
HERC2, SLC24A5, SLC25A2 - R squared: 76.4%... (HERC2 appears to be doing the vast majority of the explaining)
The obvious remaining question from all this is how high does the proportion of variance explained go if you use information from all markers together. Anyway, it appears that, as they mention, five SNPs in five genes account for much of the variation.
Given that most subjects were Eur, it would have been nice to see the extent to which they were driving the results, by for example, doing the same analysis only on them. In other words how different would the results be if most subjects were African or Native American etc...?
I did not know that HERC2 is adjacent (5' side) to OCA2, and contains a promoter region for OCA2.
Predicting Phenotype from Genotype: Normal Pigmentation
Valenzuela RK, Henderson MS, Walsh MH, Garrison NA, Kelch JT, Cohen-Barak O, Erickson DT, John Meaney F, Bruce Walsh J, Cheng KC, Ito S, Wakamatsu K, Frudakis T, Thomas M, Brilliant MH.
J Forensic Sci. 2010 Feb 11. [Epub ahead of print]
Abstract:Genetic information in forensic studies is largely limited to CODIS data and the ability to match samples and assign them to an individual. However, there are circumstances, in which a given DNA sample does not match anyone in the CODIS database, and no other information about the donor is available. In this study, we determined 75 SNPs in 24 genes (previously implicated in human or animal pigmentation studies) for the analysis of single- and multi-locus associations with hair, skin, and eye color in 789 individuals of various ethnic backgrounds. Using multiple linear regression modeling, five SNPs in five genes were found to account for large proportions of pigmentation variation in hair, skin, and eyes in our across-population analyses. Thus, these models may be of predictive value to determine an individual's pigmentation type from a forensic sample, independent of ethnic origin.