Skip to main content

Table 2 Most significant SNPs in 33 genomic regions associating at the p < 10−6 level with sporadic, BRCA-mutation-negative breast cancer cases in the Sardinian population

From: Genome-wide association study of susceptibility loci for breast cancer in Sardinian population

Chromosomal region SNP Position Alleles Frequency RSQR OR (CI 95%) p Gene
Cases Controls
1p35.1 rs9425977 34238042 C/T 0.082 0.059 0.379 2.597 (1.817 - 3.709) 9.51E-08 CSMD2
1p34.1 rs2477618 44271050 C/G 0.077 0.058 0.416 2.312 (1.647 -3.245) 9.13E-07 -
1p13.3 rs345299 108249656 A/C 0.465 0.534 0.957 0.755 (0.676 - 0.845) 9.40E-07 VAV3
1q32.1 rs6661074 203605742 A/G 0.483 0.425 0.731 1.408 (1.235 - 1.605) 3.10E-07 LEMD1
2p25.3 rs13393791 3239073 C/T 0.074 0.039 0.989 1.862 (1.469 - 2.361) 1.99E-07 TSSC1
2p21 rs17032957 45134208 A/G 0.701 0.747 0.462 0.597 (0.500 - 0.712) 9.17E-09 SIX2/SIX3
2q37.1 rs838436 232291757 A/G 0.908 0.926 0.308 0.415 (0.291 - 0.592) 8.45E-07 -
3p14.1 rs9810816 67158548 C/G 0.935 0.955 0.404 0.368 (0.251 - 0.541) 1.86E-07 -
5q35.2 rs17076993 173564400 C/T 0.071 0.049 0.447 2.507 (1.768 - 3.553) 1.29E-07 -
6q23.1 rs3777428 130495535 C/T 0.926 0.952 0.720 0.509 (0.387 - 0.668) 8.48E-07 L3MBTL3
7p14.2 rs6968002 36531229 C/T 0.938 0.958 0.533 0.431 (0.308 - 0.603) 6.32E-07 AOAH
8q24.3 rs11785598 144537061 C/T 0.948 0.929 0.328 3.420 (2.223 - 5.266) 6.40E-09 RHPN1
9q22.32 rs10512243 97815280 A/G 0.093 0.056 0.913 1.754 (1.411 - 2.181) 2.78E-07 -
9q31.2 rs10979327 110160516 G/T 0.112 0.060 0.632 3.851 (2.955 - 5.016) 2.92E-25 -
9q33.3 rs1928482 125472269 C/T 0.361 0.303 0.978 1.362 (1.206 - 1.538) 4.87E-07 DENND1A
9q34.13 rs1633769 134869098 C/G 0.769 0.803 0.393 0.558 (0.452 - 0.690) 6.07E-08 -
9q34.3 rs3811159 136828478 A/G 0.608 0.661 0.683 0.706 (0.616 - 0.810) 6.07E-07 COL5A1
10q21.1 rs1903974 53549083 A/G 0.047 0.077 0.865 0.527 (0.409 - 0.680) 4.38E-07 PRKG1
11p12 rs7947387 38902742 A/G 0.050 0.069 0.333 0.347 (0.230 - 0.523) 2.45E-07 -
12q21.1 rs11178748 70021794 A/G 0.100 0.078 0.897 1.673 (1.366 - 2.046) 5.15E-07 TSPAN8
12q23.3 rs7488485 105789959 C/T 0.097 0.073 0.404 2.348 (1.722 - 3.198) 3.17E-08 RIC8B
13q21.1 rs9569528 56234110 C/T 0.074 0.051 0.492 2.481 (1.782 - 3.456) 5.27E-08 -
14q23.1 rs17097373 59896563 C/T 0.076 0.058 0.770 1.861 (1.448 - 2.391) 9.43E-07 -
15q12 rs17651375 25763160 C/T 0.084 0.056 0.934 1.761 (1.417 - 2.189) 2.93E-07 OCA2
16q12.1 rs2193094 51123955 G/T 0.557 0.478 0.982 1.337 (1.198 - 1.491) 1.70E-07 TOX3
16q21 rs8045513 60720397 A/T 0.059 0.088 0.606 0.430 (0.326 - 0.569) 9.49E-10 -
18p11.22 rs17436811 10080771 C/T 0.084 0.058 0.644 2.002 (1.536 - 2.608) 2.20E-07 -
19q13.31 rs17725531 49018018 G/T 0.140 0.099 0.930 1.560 (1.311 - 1.858) 5.82E-07 -
20p12.2 rs6039942 10376146 A/G 0.100 0.068 0.623 2.005 (1.565 - 2.565) 2.13E-08 C20orf94
21q22.11 rs2833424 31774071 A/G 0.293 0.239 0.985 1.365 (1.206 - 1.544) 8.42E-07 TIAM1
21q22.11 rs963950 33438577 C/T 0.930 0.883 0.986 1.742 (1.432 - 2.119) 1.24E-08 IFNAR2
21q22.13 rs857989 38042001 C/G 0.154 0.111 0.896 1.537 (1.301 - 1.816) 3.72E-07 KCNJ6
22q12.3 rs6000351 35340813 A/G 0.093 0.069 0.445 2.100 (1.556 - 2.835) 7.44E-07 CACNG2
  1. The table reports, for each SNP, the genomic cytoband, the rs name, the position in build36, the corresponding alleles, the frequency in cases and controls, the imputation quality, the OR and its confidence interval, the pvalue and the most candidate gene within 200 kb. Additional SNPs in the same genomic regions are listed in Additional file 3: Table S2.