Supplementary Table 1. Hypermethylated loci in estrogen-pre-exposed stem/progenitor-derived epithelial cells. Entrez Gene Probe genomic location* Control# Pre-exposed# Description Gene ID name chr5:134392762-134392807 5307 PITX1 -0.112183718 6.077605311 paired-like homeodomain transcription factor 1 chr12:006600331-006600378 171017 ZNF384 -0.450661784 6.034362758 zinc finger protein 384 57121 GPR92 G protein-coupled receptor 92 chr3:015115848-015115900 64145 ZFYVE20 -1.38491748 5.544950925 zinc finger, FYVE domain containing 20 chr7:156312210-156312270 -2.026450994 5.430611412 chr4:009794114-009794159 9948 WDR1 0.335617144 5.352264173 WD repeat domain 1 chr17:007280631-007280676 284114 TMEM102 -2.427266294 5.060047786 transmembrane protein 102 chr20:055274561-055274606 655 BMP7 0.764898513 5.023260524 bone morphogenetic protein 7 chr10:088461669-088461729 11155 LDB3 0 4.817869864 LIM domain binding 3 chr7:005314259-005314304 80028 FBXL18 0.921361233 4.779265347 F-box and leucine-rich repeat protein 18 chr9:130571259-130571313 59335 PRDM12 1.123111331 4.740306098 PR domain containing 12 chr2:054768043-054768088 6711 SPTBN1 -0.089623066 4.691756995 spectrin, beta, non-erythrocytic 1 chr10:070330822-070330882 79009 DDX50 -2.848748309 4.691491169 DEAD (Asp-Glu-Ala-Asp) box polypeptide 50 chr1:162469807-162469854 54499 TMCO1 1.495802762 4.655023656 transmembrane and coiled-coil domains 1 chr2:080442234-080442279 1496 CTNNA2 1.296310425 4.507269831 catenin (cadherin-associated protein), alpha 2 347730 LRRTM1 leucine rich repeat transmembrane neuronal 1 chr1:042816934-042816987 4904 YBX1 0.088776519 4.495984562 Y box binding protein 1 chr20:044751602-044751647 112858 TP53RK -0.891062327 4.436484463 TP53 regulating kinase chr19:042261146-042261191 147923 ZNF420 -1.7979144 4.321177101 zinc finger protein 420 chr3:061521967-061522014 5793 PTPRG 1.2291677 4.237829771 protein tyrosine phosphatase, receptor type, G chr22:048600733-048600778 9889 ZBED4 0.34776545 4.183370855 zinc finger, BED-type containing 4 chr1:063497644-063497703 0 4.165474705 chr4:142411142-142411187 57484 RNF150 0.107319494 4.141458153 ring finger protein 150 chr17:002539774-002539819 23277 KIAA0664 0.68755446 4.137010647 KIAA0664 chr20:054638489-054638535 7022 TFAP2C 0.562945412 4.133648881 transcription factor AP-2 gamma chr11:075833207-075833258 56946 C11orf30 0.204044031 4.104957159 chromosome 11 open reading frame 30 chr22:048330412-048330459 0.720341093 4.014749777 chr16:025030484-025030529 51451 LCMT1 0.068896005 3.852987637 leucine carboxyl methyltransferase 1 chr3:053855140-053855185 55540 IL17RB -0.33802645 3.698757049 interleukin 17 receptor B 55349 CHDH choline dehydrogenase chr13:047789025-047789070 5925 RB1 -0.085901601 3.664953161 retinoblastoma 1 (including osteosarcoma) chr3:010251208-010251253 3656 IRAK2 -0.562734894 3.604471701 interleukin-1 receptor-associated kinase 2 chr15:041000713-041000770 146057 TTBK2 -1.017021165 3.592982758 tau tubulin kinase 2 chr4:013225054-013225099 0.248316279 3.58191584 chr1:090903244-090903289 0.658844243 3.574661326 chr10:111959093-111959143 4601 MXI1 0.267636537 3.566586884 MAX interactor 1 chr2:104919065-104919114 -1.19768317 3.502613025 Entrez Gene Probe genomic location* Control# Pre-exposed# Description Gene ID name chr3:036961783-036961828 -1.450582421 3.486571582 chr3:141884566-141884617 287015 TRIM42 -0.404862117 3.470429413 tripartite motif-containing 42 chr20:054400955-054401010 1477 CSTF1 0.541746739 3.463611647 cleavage stimulation factor subunit 1 6790 STK6 aurora kinase A chr12:113303987-113304047 6910 TBX5 1.419170558 3.460274721 T-box 5 chrX:152589739-152589787 57595 PDZD4 -1.040754735 3.427331954 PDZ domain containing 4 chr16:074239053-074239104 54386 TERF2IP 1.037943338 3.397449609 telomeric repeat binding factor 2, interacting protein 3735 KARS lysyl-tRNA synthetase chr7:090541197-090541242 8321 FZD1 -1.593529038 3.378354909 frizzled homolog 1 (Drosophila) wingless-type MMTV integration site family, member chr3:055496465-055496525 7474 WNT5A 0.875195991 3.355084023 5A chr7:148908004-148908049 168544 ZNF467 -0.718466725 3.312450877 zinc finger protein 467 chrX:048532866-048532926 11040 PIM2 0.081525699 3.240311988 pim-2 oncogene chr4:175579652-175579706 80817 KIAA1712 -0.496953992 3.221143024 KIAA1712 26269 FBXO8 F-box protein 8 chr12:102861897-102861942 6996 TDG 0.98608753 3.154607896 thymine-DNA glycosylase chr3:187561710-187561765 1608 DGKG 0.84407774 3.123007724 diacylglycerol kinase, gamma 90kDa chr7:026907480-026907525 3198 HOXA1 -0.495953406 3.095005637 homeobox A1 chr1:148067326-148067373 57592 ZNF687 -0.448548466 3.086631773 zinc finger protein 687 chr14:021049339-021049390 56339 METTL3 0.395823627 3.032608072 methyltransferase like 3 chr1:025003391-025003441 864 RUNX3 -1.016189553 3.01869822 runt-related transcription factor 3 chr19:063553325-063553371 503538 FLJ23569 1.116803981 3.012681196 BC040926 1 A1BG alpha-1-B glycoprotein chr15:039015828-039015873 54567 DLL4 -0.580946517 2.997730441 delta-like 4 (Drosophila) chr13:098650617-098650662 337867 PHGDHL1 -1.28948333 2.967636564 UBA domain containing 2 chrX:039762972-039763017 -0.309681229 2.942323886 chr9:137449365-137449410 54863 FLJ20245 -0.101451753 2.930690215 chromosome 9 open reading frame 167 chr19:003551280-003551325 6915 TBXA2R 0.250492144 2.900512725 thromboxane A2 receptor chrX:150014320-150014369 9248 GPR50 -0.250756805 2.83080234 G protein-coupled receptor 50 chr4:084077214-084077259 79966 SCD5 1.089023862 2.829490987 stearoyl-CoA desaturase 5 chr3:024512242-024512287 7068 THRB 1.291285855 2.788746329 thyroid hormone receptor, beta chr15:080122616-080122661 84206 RKHD3 1.288657655 2.76269307 ring finger and KH domain containing 3 chr2:122123682-122123729 23332 CLASP1 -0.0757216352.712523967 cytoplasmic linker associated protein 1 chr1:243790687-243790737 84838 ZNF496 -0.2842422 2.685882382 zinc finger protein 496 chr21:042979357-042979408 5152 PDE9A 0.123685317 2.624271817 phosphodiesterase 9A chr1:225090221-225090268 200107 FLJ31401 0.232666922 2.621164503 hypothetical protein FLJ31401 574029 DUSP5P dual specificity phosphatase 5 pseudogene chr5:000104307-000104359 -0.362033729 2.614971988 chr12:056374074-056374133 10956 OS9 -1.59401999 2.578938713 amplified in osteosarcoma chr6:167283818-167283870 0.172932602 2.550975145 Entrez Gene Probe genomic location* Control# Pre-exposed# Description Gene ID name chr7:016339679-016339728 25928 SOSTDC1 -0.410989559 2.544224252 sclerostin domain containing 1 chr17:001901955-001902000 -0.747702291 2.529820947 chr14:049135324-049135369 122769 PPIL5 -0.392227131 2.522634792 peptidylprolyl isomerase (cyclophilin)-like 5 chr10:035969628-035969673 8325 FZD8 0.175766627 2.517275693 frizzled homolog 8 (Drosophila) reprimo, TP53 dependent G2 arrest mediator chr2:154160400-154160445 56475 RPRM -0.120005751 2.510801325 candidate chr6:044351420-044351465 -0.004412416 2.459431619 chrX:131816623-131816668 90161 HS6ST2 1.328888425 2.449591193 heparan sulfate 6-O-sulfotransferase 2 chr12:021545932-021545984 51026 GOLT1B 1.448123641 2.441327786 golgi transport 1 homolog B (S. cerevisiae) 5965 RECQL RecQ protein-like (DNA helicase Q1-like) chr2:063192875-063192920 5013 OTX1 0.303037171 2.423589591 orthodenticle homeobox 1 chr9:037026850-037026895 -0.736277206 2.2761096 chr9:135617752-135617797 51116 MRPS2 0.775981707 2.270528942 mitochondrial ribosomal protein S2 chr11:022603583-022603628 2188 FANCF -0.38266565 2.247927513 Fanconi anemia, complementation group F chr19:046763214-046763259 -0.305677715 2.197088301 chr19:004075078-004075123 5605 MAP2K2 0.059248882 2.15796136 mitogen-activated protein kinase kinase 2 chr19:044032796-044032841 3191 HNRPL -1.033266259 2.140860395 heterogeneous nuclear ribonucleoprotein L early growth response 2 (Krox-20 homolog, chr10:064246532-064246582 1959 EGR2 -0.931111704 2.133348048 Drosophila) chr3:035655553-035655598 10777 ARPP-21 -0.734235565 2.100946198 cyclic AMP-regulated phosphoprotein, 21 kD chr16:066828069-066828114 80004 RBM35B 0.292766965 2.053111336 RNA binding motif protein 35B chr19:045596393-045596438 57716 PRX 0.286967596 2.049716456 periaxin chr19:004742518-004742563 55527 FEM1A -0.390849153 2.044394119 fem-1 homolog a (C. elegans) chr8:100095032-100095077 157680 VPS13B 0.209194091 1.98951254 vacuolar protein sorting 13 homolog B (yeast) chr22:036674101-036674146 5435 POLR2F 1.119372056 1.973992205 polymerase (RNA) II (DNA directed) polypeptide F 84645 C22orf23 chromosome 22 open reading frame 23 chr6:127838400-127838445 9729 KIAA0408 0.077406463 1.939520326 KIAA0408 387104 C6orf174 chromosome 6 open reading frame 174 chr2:236869638-236869693 -0.363379146 1.926191613 chr5:065256618-065256666 55914 ERBB2IP 0.179710481 1.907775975 erbb2 interacting protein chr17:070797324-070797369 60386 SLC25A19 0.481796529 1.898505189 solute carrier family 25, member 19 chr14:037138040-037138085 -0.03955225 1.871924304 chr14:068330532-068330577 677 ZFP36L1 0.001197193 1.861835952 zinc finger protein 36, C3H type-like 1 chr14:094304647-094304692 145258 GSC 0.333210027 1.856492354 goosecoid chr12:055918310-055918355 56901 LOC56901 0.455616401 1.826414967 NADH dehydrogenase 1 alpha subcomplex, 4-like 2 chr19:018867391-018867436 2657 GDF1 0.116565674 1.820215719 growth differentiation factor 1 10715 LASS1 LAG1 homolog, ceramide synthase 1 (S. cerevisiae) chr7:022826983-022827028 84668 FAM126A -0.592585118 1.710967304 family with sequence similarity 126, member A chr2:011836925-011836970 23175 LPIN1 -0.984281646 1.693560454 lipin 1 chr18:009465013-009465058 10928 RALBP1