Comparing and identifying phenotypic differences between genetically close-related populations is interesting but challenging. Here we attempt to understand the difference between Han Chinese and Japanese via the analysis of gene expression data which we assume to be a proxy measure of phenotypic differences. We first identified expression showing significant differences between the two populations (about 4.4% of the transcriptome). Next we established association between variants on DNA level and the differential expression. Our analysis showed that genetic differences can explain 7 – 43% of the identified expression differences, many of which are associated with hematological and biochemical traits, or possibly height. (By Dr. Shuhua Xu, http://jmg.bmj.com/content/early/2013/06/03/jmedgenet-2012-101501 )