Allele-Specific ENCODE ElementsPanel A shows representative allele-specific information from GM12878 cells for selected assays around the first exon of the NACC2 gene (genomic region chr9:138,950,000- 138,995,000, GRCh37). Transcription signal is shown in green, and the three sections show allele specific data for three datasets (POLR2A, H3K79me2 and H3K27me3 ChIP-seq). In each case the purple signal is the processed signal for all sequence reads for the assay, while the blue and red signals show sequence reads specifically assigned to either the paternal or maternal copies of the genome, respectively. The set of common SNPs from dbSNP, including the phased, heterozygous SNPs used to provide the assignment, are shown at the bottom of the panel. NACC2 has a statistically significant paternal bias for POLR2A and the transcription associated mark H3K79me2, and has a significant maternal bias for the repressive mark H3K27me3. Panel B shows pairwise correlations of allele specific signal within single genes (below the diagonal) or within individual ChromHMM segments across the whole genome for selected DNase-seq and histone modification and TF ChIP-seq assays. The extent of correlation is coloured according to the heatmap scale indicated from positive correlation (red) through to anti-correlation (blue).
