removed and probes with a detection P value > 0.05 in at least 1% samples or/and a beadcount < 3 in 5% of samples were removed across all samples to control for poor quality probes. The dasen function was used to normalize the data as previously described43. Cross-hybridizing probes44,45, probes with any SNP within 10bp of the CpG site or single base extension44 and probes on the sex chromosomes were excluded from the QTL analysis. These data are publically available through GEO and can be found under accession numbers: GSE58885, GSE61431, GSE61380. Genotype data is available to access from dbSNP. All fetal brain mQTL data are also available via an online database at http://epigenetics.essex.ac.uk/mQTL/.
