Allelic specificity of CTCF and H3K9me3. Informative ChIP templates were analyzed using the TaqMan allelic discrimination assay to address the allelic association of CTCF and H3K9me3. (A) Genotyping results at rs11870560 identify informative cell lines useful for the detection of allele-specific association of CTCF and H3K9me3. gDNA obtained from monoallelic and biallelic cell lines were genotyped using the TaqMan allelic discrimination assay. Squares represent gDNA samples and are coded in red and green to represent cell lines that are homozygous for allele C and allele T, respectively. Orange indicates heterozygous individuals. Averaged triplicate of a no-template control (NTC) is shown near the origin of the graph. (B) Genotyping at SNP rs11870560 with DNA templates recovered from ChIP experiments was used to identify the enrichment of the two alleles with either CTCF (circle) or H3K9me3 (triangle). Each color shown in the figure key represents a lymphoblastoid cell line (LCL) derived from an individual of the pedigree, while the shape represents the source of each sample (for example, squares signify input samples, while circles and triangles indicate ChIP samples obtained with CTCF and H3K9me3 antibodies, respectively). Immunoprecipitated templates were generated using the ChIP protocol described in Materials and Methods. Both monoallelic and biallelic cell lines indicate biallelic distribution of both CTCF and H3K9me3. Diamonds indicate control LCL samples (standards) previously genotyped as homozygous CC, heterozygous CT and homozygous TT.