Imputation demonstrates that rs10784774 forms the 5′ SNP in a haplotype spanning LYZ of 4 SNPs in almost complete LD (Supplementary Figure 11). Analysis of ENCODE ChIP-seq data24 demonstrates a p300 binding site overlapping rs10784774 and further sites overlapping the promoter (Supplementary Figure 12). To investigate the allelic relationship between p300 and LYZ expression, genotype conditioned correlation analysis between basal expression of p300 and LYZ was performed. We observed a strong inverse correlation between expression of p300 and LYZ expression in individuals homozygous with the ancestral A allele at rs10784774 but no association with expression in the homozygous G allele (AA: r2 0.41, p=4.4×10−8; AG: r2 0.22, p=1.4×10−9; GG: r2 0.02, p=0.11), supportive of allele-specific regulation of LYZ via p300.
