To identify cis-acting eQTL effects on expression of ZNF804A, we assayed mRNA samples from 34 individuals heterozygous for non synonymous SNP rs4667001 (figure 3). The G allele at this locus was associated with a 1.13 fold increase (SD =0.08) in ZNF804A expression (t-test P=2.59×10−7, unequal variance). rs4667001 has D’=1 with rs1344706 in this sample. The higher expression G allele is always in phase with risk allele rs1344706T, this haplotype representing ~75% of all rs1344706T risk alleles. The under-expressed A allele at rs4667001 resides on a mixture of haplotypes of which the majority (>70%) carry the non-risk allele rs1344706G. Thus, consistent with our analysis of the GeneVar data, the risk allele at rs1344706 is generally carried by a higher ZNF804A expression haplotype. If rs1344706 is per se the eQTL responsible for association between that SNP and ZNF804A expression, we expect only those subjects that are heterozygous for it to show unequal allelic expression (since homozygotes for rs1344706 would carry two functionally equivalent eQTL alleles). Our observed data were not compatible with this, there being no difference in the degree of differential
