Figure 3: The non-coding landscape and eQTL associations for the rs2077606 susceptibility SNP at 17q21.31.

(a) Analysis of the chromatin landscape at ARHGAP27 and PLEKHM1 in normal ovarian surface epithelial and fallopian tube secretory epithelial cells (OSECs/FTSECs) by formaldehyde-assisted isolation of regulatory elements sequencing (FAIRE-seq). Alignment with ENCODE FAIRE-seq tracks (shown) and ChIP-seq tracks (not shown) from non-EOC-related cell lines reveals open chromatin peaks corresponding to (a) promoters (b) CTCF insulator binding sites and (c) H3K4me3 signals, suggestive of a dynamic regulatory region. An H3K4me3 signal at a coding ARHGAP27 mRNA variant (c) located between the genes is highly pronounced in OSEC/FTSEC, suggesting tissue-specific expression and function. Several of the top-ranking SNPs fall within TFBS (Supplementary Table S2). rs12942666 did not coincide with TFBS, but tightly linked SNPs, rs12946900 and rs2077606 fell within predicted binding sites for SPIB and ZEB1, respectively. (b) We analysed the expression of SPIB and ZEB1 in primary high-grade serous tumours from TCGA and found (i) no significant change in SPIB expression but (ii) significant downregulation of ZEB1 in tumours compared with normal tissues. (iii) QPCR analysis of ZEB1 expression in 73 OCPT and 50 EOC cell lines supported the finding that ZEB1 expression is lower in cancer cell lines compared with normal precursor tissues. (c) eQTL analysis in OSECs/FTSECs for different alleles of rs2077606. (i) There was a significant eQTL for ARHGAP27, with the minor (A) allele being associated with increased ARHGAP27 expression. (ii) There was no evidence of an association between rs2077606 genotypes and ARHGAP27 expression in lymphoblastoid cell lines, suggesting this association may be tissue-specific. (iii) We observed a borderline significant eQTL association between ZEB1 mRNA and rs2077606 in tumours from TCGA, with the minor risk allele also associated with lower expression.