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Table 1 Distribution, minor allele frequencies and functional prediction of the selected breast cancer common variants

From: A genome wide SNP genotyping study in the Tunisian population: specific reporting on a subset of common breast cancer risk loci

Locus Marker ID Alleles GMA GMAF TUN (freq) Location Score eQTL associations Predicted function
1q32.1 rs4245739 A/C C 0.2141 0,333 Intergenic 6 No association 3UTR MDM4 miR-191 target site and results in decreased MDM4 expression
2p24.1 rs12710696 T/C T 0.4455 51,1 Intergenic 4 No association TF binding and DNase peak
2q31.1 rs1550623 A/G G 0.1711 0,24 Intergenic 4 No association TF binding and DNase peak
4q21 rs1494961 C/T C 0.3355 52,6 Exonic HELQ c.916G > A 1f No association Tolerated
4q21 rs11099601 C/T C 0.33613 53,4 3 UTR FAM175A c.413 C > T 1f p = 1.94 × 10−21 with MRPS18C DAE eQTL and TF binding / DNase peak
4q34.1 rs6828523 C/A A 0.2468 0,179 Intronic, ADAM29 c.-450-5711C > A No data No association No data
6p23 rs204247 A/G G 0.4321 0,37 Intergenic (11 kb 5′-RANBP9) 6 No association Minimal functional evidence
6q25.1 rs2046210 G/A A 0.4121 0,45 Intergenic, 6 kb 3’-CCDC170 6 No association Minimal functional evidence
7q35 rs720475 G/A A 0.1478 0,263 Intronic; ARHGEF5 c.4531 + 646G > A 5 p = 1.4 × 10−6 with ARHGEF34P gene and p = 4.2 10− 6 for OR2A9P gene TF binding or DNase peak
9q31.2 rs10759243 C/A A 0.4607 0,477 Intergenic (53 kb 5′-KLF4) No data No association No data
10p12.31 rs7072776 G/A A 0.3055 0,441 Intergenic (382 bp 3′ MLLT10) 5 No association TF binding or DNase peak
10p15.1 rs2380205 C/T T 0.3750 0,48 Intergenic, 2.6 kb 5′-GDI2 3a No association TF binding, any motif and DNase peak
10q22.3 rs704010 C/T T 0.2674 0,322 Intronic; ZMIZ1 c.-337 + 12,121 T > C 2b No association TF binding, any motif, DNase Footprint and DNase peak
10q26 rs1219648 A/G G 0.4089 0,466 Intronic; FGFR2 c.109 + 7033 T > C No data No association No data
10q26 rs2981582 G/A A 0.4038 0,463 Intronic, FGFR2 c.109 + 906 T > C 5 No association TF binding or DNase peak
11q13.1 rs3903072 G/T T 0.3165 0,467 Intergenic (7.4 kb 3′-CFL1) 4 p = 9 × 10−6 for SNX32, and p = 2.9 × 10− 5 for CTSW TF binding and DNase peak
11p15.5 rs3817198 T/C C 0.2155 0,277 3UTR LSP1 c. 13 + 200 T > C 5 No association TF binding or DNase peak
12q24.21 rs1292011 A/G G 0.4211 0,469 Intergenic 4 No association TF binding and DNase peak
14q24.1 rs2588809 C/T T 0.1831 0,298 Intronic RAD51B c.757–98,173 T > C No data No association No data
14q32.11 rs941764 A/G G 0.4193 0,468 Intronic CCDC88C c.271–15,014 T > C 4 No association TF binding and DNase peak
16q12.1 rs3803662 G/A A 0.4403 0,414 Intergenic, 5′ to TOX3 5 No association TF binding or DNase peak
16q12.1 rs8051542 C/T T 0.3133 0,396 Intronic TOX3 c.88–3168 A > G 5 No association TF binding or DNase peak
16q23.2 rs13329835 A/G G 0.2957 0,376 Intronic CDYL2 c.1007 + 3855 T > C 4 No association TF binding and DNase peak
17q21 rs9911630 A/G G 0.4972 0,426 3’of BRCA1 NC_000017.10:g.41188342A > G 1b p = 1.2 × 10−23 for NBR2 and p = 1.3 × 10−6 for CTD-3199 J23.6 and p = 6.1 × 10−6 for LINC00854 eQTL, TF binding, any motif, DNase Footprint and DNase peak
17q21 rs799916 T/G T 0.4976 0,404 Intronic BRCA1 c.4097-141A > C 6 p = 2.1 × 10−25 for NBR2 p = 8.3 × 10−7 for CTD-3199 J23.6 and p = 3.7 × 10−6 for LINC00854 Minimal functional evidence
18q11.2 rs1436904 T/G G 0.3568 0,292 Intronic CHST9 c.202 + 33413A > C No data No association No data
19p13.11 rs4808801 A/G G 0.4521 0,404 Intronic ELL c.744 + 1247 T > C 1f p = 1.6 × 10−5 for SSBP4 eQTL, TF binding and/or DNase peak
22q13.1 rs6001930 T/C C 0.1414 0,109 Intronic MKL1 c.-59-16944A > G 5 No association TF binding or DNase peak
  1. -GMA Global Minor Allele, GMAF Global Minor Allele Frequency, TUN (freq) the frequency of the global minor allele in the Tunisian population, Score: from the RegulomeDB database and score significance provided in the predicted function column, eQTL association provided by the GTEx database, p the p value of the variants’ eQTL association, TF Transcription factor
  2. -The highlighted rows indicate polymorphisms that showed the highest RegulomeDB scores, significant eQTL associations and other functional evidence
  3. -rs1494961 is the only exonic variant in this list, we provided its predicted functional significance using the Sift software
  4. -In bold, SNPs previously identified as associated with breast cancer risk in the Tunisian population