To examine relationships between genetic variants and local gene expression levels in lymphoblastoid cell lines, we performed cis-acting expression of quantitative locus (cis-eQTL) analysis. These relationships included those between all replicable risk SNPs in PHF3 and PHF3 mRNA expression levels, and those between all replicable risk SNPs in PTP4A1 and PTP4A1 mRNA expression levels. Expression data of 14,925 transcripts (14,072 genes) in 270 unrelated HapMap individuals from six populations [Utah residents with Northern and Western European ancestry from the CEPH collection (CEU)-Children, CEU-Parent, Han Chinese in Beijing (CHB), Japanese in Tokyo (JPT), Yoruba in Ibadan (YRI)-Children and YRI-Parent] were evaluated [13]. Differences in the distribution of mRNA expression levels between SNP genotypes were compared using a Wilcoxon-type trend test. P-values less than 0.05 were listed in Table 1 and plotted in Figure 1 . Additionally, effects of SNPs 1 Mb surrounding the association peak SNP (rs9294269) were illustrated in Figures 1D–H .
