Table 1.

MCF-7 breast cancer risk enhancers; listed are the 10 best breast cancer risk loci in MCF-7 and the corresponding 10 MCF-7 risk enhancers that are most suitable for follow-up testing

LocusAlt. locus IDCRVs Enh. overlapCRVs in locusHyper. P val. (-log)Ratio enrich.Span overlap signif. (-log)Lead SNP IDComb. GWAS P val.Comb. GWAS P val., ER Pos.Risk enhancer startRisk enhancer stopGeneMCF-7 DE Genes 0–500 KbMCF-7 DE Genes 500 Kb–1 Mb
1p36.221_105662158504.295.791.72rs25068892.38E-201.10E-071059587710599012PEX14APITD1, TARDBP, UBE4B, PEX14SRM, SLC25A33, PIK3CD, LZIC, PTCHD2, CLSTN1, EXOSC10, MTOR
3p26.13_47422761220.653.311.71rs67873919.07E-191.20E-1547278724732087EGOT, ITPR1BHLHE40, ARL8B, ITPR1, SUMF1EDEM1
6q256_151952332101012.5017.642.19rs609540782.84E-541.70E-22151948050151959756ESR1ZBTB2, RMND1, AKAP12, C6orf211, SYNE1, ESR1MTHFD1L, PLEKHG1
8q22.38_102478959281.506.621.66rs5141925.61E-099.90E-09102478133102481107YWHAZ, GRHL2, KLF10ZNF706, GRHL2ANKRD46, YWHAZ, RRM2B, UBR5, PABPC1
10p1410_9088113304223.508.932.15rs679580071.73E-106.00E-0890743929089320GATA3N/AGATA3
12q24.3112_1208321462260.802.321.54rs2069663.79E-081.40E-06120831824120833249DYNLL1, GATCTRIAP1, SRSF9, POP5, PXN, MSI1, DYNLL1, COQ5, UNC119B, CCDC64, RNF10PRKAB1, P2RX4, CIT, ANAPC5
16q23.216_806508058179.6926.122.66rs75000674.06E-272.90E-218064714780651103CDYL2ATMIN, CENPN, CDYL2GAN, CMIP
17q25.317_777817253132.569.981.90rs80824521.14E-102.40E-067776976977772332N/ACBX2, CBX8, CBX4, CARD14, SGSH, SLC26A11, TBC1D16, EIF4A3TIMP2, LGALS3BP, ENDOV, USP36, RPTOR
19p13.1219_13954571194313.358.742.74rs25947141.08E-081.70E-051394890213955856JUNB, NANOS3MIR24-2, PALM3, SAMD1, CCDC130, ZSWIM4, C19orf57, PODNL1, ASF1B, IL27RA, LPHN1CALR, SYCE2, TRMT1, CD97, GIPC1, DNAJB1, HOOK2, MAST1, NFIX, PKN1, ZNF333
21q21.121_16520832224.32143.222.52rs24039071.87E-324.20E-231657027816574820NRIP1NRIP1HSPA13, USP25
  • NOTE: Each enhancer overlaps the most significant GWAS SNP at the locus, and the locus shows both an enrichment greater than 2 (frequency of breast cancer CRVs overlapping enhancers compared with background overlap frequency), as well as a proportion of the CRV risk span that overlaps enhancers greater than more than 95% background overlap proportions. The enrichment and overlap values may be modified by overlap of risk SNPs with other enhancers at the same locus. The overall GWAS significance, ER+ GWAS significance, and reported genes from Michailidou and colleagues are listed. In addition, all but the enhancer at locus 19 are unique to MCF-7 and do not overlap HMEC enhancers locations, so the differentially expressed genes (relative to HMEC) within 500 Kb or 1 MB of each lead SNP are identified as putative risk genes in MCF-7.

  • Abbreviation: N/A, not applicable.