Skip to main content
Fig. 2 | Genome Biology

Fig. 2

From: Spatial chromatin architecture alteration by structural variations in human genomes at the population scale

Fig. 2

Predicting the impact of SVs on the chromatin topology. a Browser view of a 0.5-Mb genomic segment with asthma-associated SNP rs12936231 identified in a part of the human population. SNP rs12936231 alters the sequence of a CTCF motif involved in interactions. Haplotype-specific CTCF signals from 10 lymphoblastoid cells are presented along with haplotype-specific CTCF ChIA-PET interactions from GM12878 (only a subset of all interactions can be identified as specifically paternal/maternal as it is done based on allele-specific SNPs emerging at the interaction anchors). For each track, ChIP-seq signal values (originally in RPMs) were divided by the maximal value of the signal in the visualized region. Sum of the signal values over the genomic region occupied by the SNP-affected interaction anchor together with the genotype is marked in each signal track. b Comparison of sequences and scores of CTCF binding motifs carrying the reference C and the alternative G alleles of rs12936231. c Differences in gene transcription rates between genotypes set for rs12936231. Genes exhibiting differences in transcription which pass Mann-Whitney test with p value < 0.05 were reported. Center lines show the medians; box limits indicate the 25th and 75th percentiles; whiskers extend 1.5 times the interquartile range (IQR) from the 25th and 75th percentiles; outliers are represented by rings; far outliers (points beyond 3 times the IQR) are not represented by any element of box plots. n = 101, 227, 117 sample points. d CTCF anchors from GM12878 not intersected with CTCF ChIP-seq peaks identified in different lymphoblastoid cells. The anchors were filtered by consensus CTCF binding sites (see the “Methods” section). e Number of SVs, divided by type, intersecting (in case of interaction anchors), covering (in case of CCD boundaries), or contained in (in case of CCDs and CCD gaps) different genomic structural elements

Back to article page