Table 1.
Distribution, minor allele frequencies and functional prediction of the selected breast cancer common variants
| 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 |
-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
-The highlighted rows indicate polymorphisms that showed the highest RegulomeDB scores, significant eQTL associations and other functional evidence
-rs1494961 is the only exonic variant in this list, we provided its predicted functional significance using the Sift software
-In bold, SNPs previously identified as associated with breast cancer risk in the Tunisian population