We used two independent genome-wide SNP/ mRNA expression data sets for SNP-eQTL analyses on 12q21.31. The first data set was from pre-mortem human hippocampus of 137 individuals involved in the Epilepsy Surgery Program at Bonn University, Germany. Methods related to the hippocampal eQTL experiment are detailed in the supplemental method section The second was the publicly available GENEVAR - GENe Expression VARiation–data set of EPV-transformed lymphocytes from the 210 unrelated HapMap individuals (http://www.sanger.ac.uk/humgen/genevar/) (Stranger et al., 2005; Stranger et al., 2007). Experimental design and statistical analysis: In both data sets, we selected all RefSeq annotated genes (Pruitt et al., 2005) located within 1.5 megabase on both sides of the genome-wide significant SNP of the GWAS (rs1545843, total sequence of 3 Mb). The five following genes intersect with the defined genomic region (hybridisation probes in brackets, see also tab. S1): TMTC2 (GI_22749210-S), SLC6A15 (GI_33354280-A, GI_21361692-I, GI_33354280-I), TSPAN19 (GI_37541880-S), LRRIQ1 (hmm2373-S) and ALX1 (GI_5901917-S). For the GENEVAR data set a residual expression variable for each probe was built by regression analysis to correct for ethnicity. We tested an allelic and both alternative
