Studies of the genetics of gene expression reveal expression SNPs (eSNP) that explain variation in transcript abundance. Here we report a step-by-step protocol of a whole genome gene expression association mapping procedure using JMP Genomics (SAS Institute, Cary, NC) as described in ref. 1. The method accounts for population structure, ethnicity, relatedness and other variables and was applied on a sample of 194 individuals from a city and two villages in southern Morocco representing two ethnicities and a wide range of family relationships.