Extended Data Fig. 3: Identification of haplotype-specific chromatin architectures within HLA locus.
a, View of single-molecule haplotype-resolved genetic information, CpG methylation information and chromatin accessibility information for a heterozygous single-nucleotide variant (SNP) identified for GM12878 within the HLA locus. Note that all information is derived from the same sequencing reads. Denoted below is the location of a predicted CTCF binding element, and immediately above it are two fibers that demonstrate single-molecule protein occupancy at this site. b, Quantification of CpG methylation surrounding this SNP (top), as well as the percentage of fibers with a FIRE element overlapping that SNP (bottom), by haplotype. The box bounds the interquartile range (IQR) divided by the median, and the whiskers extend to the minima and maxima of the data. *Top, p value = 0.00077 (one-sided paired t test without adjustment for multiple comparisons, n = 8). *Bottom, p value = 0.00061 (one-sided Fisher’s exact test without adjustment for multiple comparisons).
