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Table 2 Genomic loci harbouring low-penetrance breast cancer susceptibility alleles

From: Hereditary breast cancer: ever more pieces to the polygenic puzzle

Locus SNP Reported gene Nearby genes (selected) Association with ER status Reference
1p11 rs2580520, rs11249433 EMBP1 HIST3, HIST2H2BA ER + ve ~ ER-ve [99, 101, 119, 120]
1p13 rs11552449 DCLRE1B PTPN22, HIPK1, BCL2L15 ER + ve > ER-ve [72]
1p36 rs616488 PEX14 KIF1B, UBE4B, RBP7 ER-ve > ER + ve [37]
1q32 rs4245739 MDM4 PIK3C2B ER-ve [115]
1q32 rs6678914 LGR6 UBE2T, PTPN7 ER-ve [115]
2p24 rs12710696 intergenic OSR1 ER-ve [115]
2q14 rs4849887 intergenic INHBB, RALB, GLI2 ER + ve ~ ER-ve [72]
2q31 rs2016394 intergenic DLX1, DLX2, ITGA6, PDK1 ER + ve [72]
2q31 rs1550623 intergenic CDCA7, MLK7-AS1, ZAK ER + ve ~ ER-ve [72]
2q33 rs1045485, rs10931936, rs3834129- rs6723097-rs3817578 CASP8 CASP10, ORC2, CDK15 ER + ve ~ ER-ve [101, 121, 122]
2q34 rs13393577 ERBB4 MIR4776 ER + ve ~ ER-ve [110]
2q35 rs13387042, rs16857609 DIRC3 PINC, TNS1, IGFBP1, IGFBP5 ER + ve > ER-ve [72, 97, 103, 123, 124]
3p24 rs4973768 SLC4A7 NEK10 ER + ve > ER-ve [98, 101, 103]
3p24 rs12493607 TGFBR2 GADL1 ER + ve [72]
3p26 rs10510333 intergenic GRM7 ER + ve ~ ER-ve [113]
3p26 rs6762644 ITPR1 SUMF1, BHLHE40 ER + ve [72]
3q25 rs6788895 SIAH2 MED12L, SELT, EIF2A ER + ve [112]
3q26 rs3806685 intergenic PIK3CA, ZNF639 ER + ve ~ ER-ve [110]
4q24 rs9790517 TET2 PPA2 ER + ve [72]
4q34 rs6828523 ADAM29 GLRA3 ER + ve [72]
5q11 rs889312, rs16886165 intergenic MAP3K1, MIER3 ER + ve > ER-ve [95, 99, 101]
5q11 rs1353747, rs10472076 PDE4D RAB3C, PDK2 ER + ve ~ ER-ve [72]
5p12 rs4415084, rs10941679, rs7716600, rs9790879, rs4866929 intergenic HCN1, MRPS30,FGF10 ER + ve > ER-ve [96, 97, 101, 103, 124]
5p15 rs1092913 intergenic MARCH6, DAP ER + ve > ER-ve [105, 110]
5p15 rs2736108, rs10069690, rs2242652 TERT CLPTM1L variant specific [104, 114]
5q33 rs1432679 EBF1 RNF145, UBLCP1 ER + ve ~ ER-ve [72]
6p23 rs204247 intergenic RANBP9, SIRT5, CCDC90A ER + ve [72]
6p24 rs9348512 intergenic GCNT2, PAK1IP1, TFAP2A BRCA2 specific [118]
6p25 rs11242675 intergenic FOXQ1, FOXF2, FOXC1 ER + ve ~ ER-ve [72]
6q14 rs17529111, rs17530068 intergenic FAM46A, IBTK, SSBP2 ER + ve ~ ER-ve [72, 109]
6q25 rs9498283 TAB2 SUMO4, LATS1 ER + ve ~ ER-ve [110]
6q25 rs3757318, rs12662670, rs6929137, rs3734804, rs3734805, rs2046210 intergenic ESR1 variant specific [100, 101, 103, 106, 125127]
7q32 rs2048672 FLJ43663 MIR29A, KLF14 not mentioned [106]
7q35 rs720475 ARHGEF5 NOBOX ER + ve [72]
8p12 rs9693444 intergenic DUSP4, KIF13B ER + ve ~ ER-ve [72]
8q21 rs6472903, rs2943559 HNF4G CRISPLD1, ZFHX4 ER + ve > ER-ve [72]
8q24 rs672888, rs1562430, rs13281615, rs11780156 intergenic PVT1, MIR1204-08, MYC ER + ve ~ ER-ve [72, 95, 101, 103]
9p21 rs1011970 CDKN2B CDKN2A, CDKN2B-AS1 ER + ve > ER-ve [101]
9q31 rs865686, rs10759243 intergenic RAD23B, KLF4 ER + ve > ER-ve [72, 103]
10p12 rs7072776, rs11814448 intergenic DNAJC1, MLLT10 ER + ve ≠ ER-ve [72]
10p15 rs2380205 intergenic ANKRD16, FBXO18, GDI2 ER + ve ~ ER-ve [101]
10q21 rs10822013, rs10995190 ZNF365 EGR2, NRBF2 ER + ve > ER-ve [101, 106]
10q22 rs704010, rs12355688 ZMIZ1 PPIF, ZCCHC24, EIF5AL1 ER + ve ~ ER-ve [101, 113]
10q25 rs7904519 TCF7L2 ZDHHC6, CASP7, DCLRE1A ER + ve ~ ER-ve [72]
10q26 rs2981582, rs11199914, rs2981579, rs1219648, rs10510102 FGFR2 WDR11, TACC2 ER + ve [72, 95, 96, 99, 101, 103, 124]
11p15 rs3817198, rs909116 LSP1-TNNT3 CTSD, DUSP8, IGF2 ER + ve ~ ER-ve [95, 101, 128]
11q13 rs3903072 intergenic RELA, MAP3K11, MUS81 ER + ve [72]
11q13 rs614367, rs661204, rs78540526, rs554219, rs657686, rs75915166 intergenic CCND1, FGF19, FGF4, FGF3 ER + ve > ER-ve [101, 116]
11q24 rs11820646 intergenic BARX2, NFRKB, PRDM10 ER + ve ~ ER-ve [72]
12p11 rs10771399 PTHLH CCDC81 ER + ve ~ ER-ve [108]
12p13 rs12422552 intergenic ATF7IP, GRIN2B, PLBD1 ER + ve ~ ER-ve [72]
12q22 rs17356907 intergenic NTN4, USP44, METAP2, NR2C1 VEZT, FGD6, CCDC38 ER + ve ~ ER-ve [72]
12q24 rs1292011 intergenic TBX3 ER + ve > ER-ve [108]
14q13 rs2236007 PAX9 NKX2-8 ER + ve > ER-ve [72]
14q24 rs999737, rs2588809, rs1314913, rs10483813, rs8009944, RAD51B ZFP36, ACTN1, DCAF5 ER + ve [72, 99, 101, 111, 119]
14q31 rs4322600 GALC GPR65 ER + ve ~ ER-ve [113]
14q32 rs941764 CCDC88C GPR68, SNORA11B, RPS6KA5, SMEK1, CATSPERB, TC2N ER + ve [72]
16q12 rs3803662 intergenic TNRC9/TOX3, MIR548, CHD9 ER + ve > ER-ve [95, 101, 103, 107, 111, 124]
16q12 rs17817449, rs11075995 FTO AKTIP, RBL2, CHD9 ER + ve ~ ER-ve [72, 115]
16q23 rs13329835 CDYL2 CENPN, ATMIN, GCSH, PKD1L2 ER + ve > ER-ve [72]
17q22 rs6504950, rs1156287 STXBP4 COX11, HLF ER + ve > ER-ve [98, 101]
17q24 rs11077488 intergenic KCNJ2, KCNJ16 Not mentioned [110]
18q11 rs527616, rs1436904 CHST9 KCTD1, TAF4B ER + ve > ER-ve [72]
19p13 rs8170, rs8100241, rs2363956 BABAM1 ANKLE1 ER-ve [102, 109, 129]
19p13 rs4808801 ELL SSBP4, FKBP8, PDE4C ER + ve ~ ER-ve [72]
19q13 rs3760982 intergenic ZNF Cluster, KCNN4, SMG9, XRCC1 ER + ve ~ ER-ve [72]
19q13 rs10411161, rs3848562 ZNF577 MIR125A, ZNF Cluster Not mentioned [105]
20q11 rs2284378 RALY ASIP, EIF2S2, CHMP4B, ZNF341, E2F1 ER-ve [109]
21q21 rs2823093 intergenic NRIP1 ER + ve > ER-ve [108]
22q12 rs132390 EMID1 KREMEN1, CHEK2, EWSR1, NF2 ER + ve ~ ER-ve [72]
22q13 rs6001930 MKL1 SGSM3, ADSL, MCHR1, XPNPEP3, DNAJB7, RBX1 ER + ve ~ ER-ve [72]
22q13 CNV2576, tagged by rs12628403 APOBEC3A- APOBEC3B APOBEC3C ER + ve ~ ER-ve [130]
  1. Legend to Table 2:
  2. 72 genomic loci that have been found to harbour low-penetrance breast cancer susceptibility alleles. Genes already mentioned in Table 1 have been excluded although long-range effects remain a possibility. All loci except for CASP8 have been derived from genome-wide association studies. Some chromosomal loci that harbour more than one independent risk variant were here combined when there was a strong overlap of candidate genes. If the variant was within a gene, this is listed separately, although this does not necessarily mean it represents the causal gene. Selected candidate genes in the vicinity (< 1 Mb) are listed in the fourth column. Genes were taken from the GRCh37.p10 primary assembly drawn from the NCBI Genbank (http://www.ncbi.nlm.nih.gov/gene). Association with ER status has been drawn from the original references, and a preponderance of one subtype was assumed if p(het) < 0.05. Note that genome-wide significance has been borderline for some results [106, 110, 113] so that additional validation may be needed for those variants.