Genotyping and Imputation of EBV-Infected B Cell Lines

We genotyped five EBV-infected B cell lines with available ChIP-seq data (Supplementary Table 2) on Illumina OMNI-5 arrays, as previously described^{71 (link)}. Genotypes were called using the Gentrain2 algorithm within Illumina Genome Studio. Quality control was performed as previously described^{71 (link)}. Quality control data cleaning was performed in the context of a larger batch of non-disease controls to allow for the assessment of data quality. Briefly, all cell lines had call rates >99%; only common variants (minor allele frequency >0.01) were included; and all variants were previously shown to be in Hardy-Weinberg equilibrium in control populations at P>0.0001^{71 (link)}. We performed genome-wide imputation using overlapping 150 kb sections of the genome with IMPUTE2^{72 (link)} and a composite imputation reference panel of pre-phased integrated haplotypes from 1,000 Genomes (June 2014). Included imputed genotypes met or exceeded a probability threshold of 0.9, an information measure of 0.5, and the same quality-control criteria described above for the genotyped markers.