We analysed genome-wide Illumina expression array data on the locus associated with MD on 12q21.31 in a pre-mortem human hippocampus expression study from individuals with temporal lobe epilepsy of European descent and gene expression from EPV-transformed lymphoblastoid cell lines of the 210 unrelated HapMap individuals of different human populations (CEU, CHB, JPT, YRB)(Stranger et al., 2005). Previous studies reported that the median distance between SNPs and genes whose mRNA expression is significantly regulated by them is approximately 30 kb, ranging up to a maximum of 1 Mb (Myers et al., 2007). We therefore assessed all five RefSeq annotated genes within 1.5 Mb proximal and distal of rs1545843 on 12q21.31 (fig. 1A and tab. S1, TMTC2, SLC6A15, TSPAN19, LRRIQ1, ALX1). Expression levels of all seven available probes (3 for SLC6A15) were related to genotypes of two of the SNPs associated with MD which best tag the overall associated SNPs on 12q21.31 for European populations, rs1545843 and rs1031681 (tab. 1). We tested the allelic and both alternative recessive-dominant genetic models of rs1545843 and rs1031681 and each probe and applied Bonferroni correction for
