The ALSPAC replication sample consists of 931 LCLs derived from The Avon Longitudinal Study of Parents and their Children (ALSPAC) 42. Expression profiling of the samples, each with two technical replicates, were performed using the Illumina Human HT-12 V3 BeadChips (IlluminaInc) and processed as the MuTHER samples described above. ALSPAC individuals were genotyped using the Illumina HumanHap550 genome-wide SNP genotyping platform. Markers with <1% MAF, >5% missing genotypes or which failed an exact test of Hardy-Weinberg equilibrium (P<5×10−7) were excluded from further analysis. Any individuals who did not cluster with the CEU individuals in multidimensional scaling analysis, who had >3% missing data, minimal or excessive heterozygosity (>33% or <31%), evidence of cryptic relatedness (>10% IBD) and any individuals with incorrect gender assignments were also excluded. After data cleaning 315,807 SNPs were left. Imputation was carried out using MACH 1.0.16, Markov Chain Haplotyping43, using CEPH individuals from phase 2 of the HapMap project as a reference set. Associations between SNP genotypes and normalized expression values were conducted using a linear model.
