Fig. 4
From: Systematic identification of regulatory variants associated with cancer risk
Regulatory SNP rs11055880 is in an intergenic enhancer regulating the expression of the ATF7IP gene. a Genomic context of rs11055880 shown in the integrative genome viewer. ChIA-PET signals in MCF7 cells (the interaction between rs11055880 and ATF7IP shown by the purple boxes), ENCODE annotations of DNase hypersensitive sites, H3K4me3, and H3K27ac in MCF7 cells, and DHSs and H3K4me3 marks in HEK293 cells are shown in tracks 1–6. The regulatory activities are shown in track 7. Red dots represent SNPs in PREs and the enlarged one is rs11055880. The blue dots represent SNPs in NREs and the black dots represent other tested SNPs in this region. b Activities of two alleles of rs11055880 in our screen. Two-tailed paired t-test was used, *p value = 0.047. c Activities of two alleles of rs11055880 in the luciferase reporter assay. Two tailed t-test, ***p value = 2.0 × 10−4. d Expression levels of ATF7IP by qPCR in HEK293T cells expressing sgRNAs targeting the rs11055880 loci (rs11055880-sg2 and rs11055880-sg5) after KRAB-dCas9 activation. P values were calculated by t-test compared to a non-targeting (NT) group from three replicates; *p value = 0.016, ***p value = 4.0 × 10−4. For b–d, the error bars represent standard erorrs