Putative transcription factor and methylation sites on IL28B haplotypes. The 6 haplotypes identified using Haploview are shown. SNPs changing CpG sites in the region identified as methylated by the Miklem and Hillier method (unpublished, UCSC Draft Human Genome) are boxed in red. Predicted transcription factor binding sites different between haplotypes were identified using Ali Baba . Note these recognition site differences are from in silico analyses only, and serve as a proof of principle that the haplotype sequence differences are sufficient to alter response to transcription factors.