The identified mQTLs residing in schizophrenia-associated GWAS regions do not necessarily represent the actual causal risk variants; in many instances we are likely to be capturing ‘passenger’ effects whereby the variant influencing DNA methylation and the schizophrenia-associated SNP are instead co-segregating in the same LD block. Therefore we sought to identify instances where a likely causal risk variant for schizophrenia was an mQTL SNP. We used 1000 Genomes Project data (http://www.1000genomes.org/) to identify all variants in strong LD (r2 > 0.8) with the 125 autosomal index SNPs associated with schizophrenia12. Of note, two of the actual schizophrenia GWAS index SNPs represent Bonferroni-significant fetal brain mQTLs: rs2535627 (associated with DNA methylation at cg11645453, P = 3.05×10−13, Supplementary Fig. 10) and rs4648845 (associated with DNA methylation at cg02275930, P = 4.54×10−15, Supplementary Fig. 11). 46 additional mQTL variants that are in strong LD with another six index SNPs are part of 86 highly-significant fetal brain mQTL pairs (Supplementary Table 16).
