Table 1.
Association of susceptibility loci from previous GWAS with breast cancer risk in African American women in WHI
| Chromosomal Position |
GWAS reference |
SNP | Position | Alleles1 | MAF2 | Imputed | Imputation r23 |
Discovery GWAS OR4 |
HR (95% CI) | P-value5 |
|---|---|---|---|---|---|---|---|---|---|---|
| 1p11.2 | (14) | rs11249433 | 120982136 | A/G | 0.16 | Yes | 0.6841 | 1.16 | 1.08 (0.83,1.41) | 0.56 |
| 2q35 | (12, 14, 15) | rs13387042 | 217614077 | A/G | 0.27 | Yes | 0.9925 | 0.80 | 1.07 (0.89,1.27) | 0.48 |
| 3p24.1 | (7) | rs4973768 | 27391017 | C/T | 0.21 | Yes | 0.9445 | 1.16 | 1.02 (0.86, 1.20) | 0.84 |
| 5p12 | (13) | rs10941679 | 44742255 | A/G | 0.37 | Yes | 0.9562 | 1.19 | 1.31 (1.06, 1.63) | 0.014 |
| 5q11.2 | (8, 15) | rs16886165 | 56058840 | T/G | 0.33 | Yes | 0.9688 | 1.23 | 1.05 (0.89,1.25) | 0.57 |
| 5q11.2 | (14) | rs889312 | 56067641 | A/C | 0.32 | Yes | 0.96 | 1.22 | 0.98 (0.83,1.16) | 0.79 |
| 6q22.33 | (9) | rs2180341 | 127642323 | A/G | 0.31 | Yes | 0.9989 | 1.41 | 0.98 (0.83,1.17) | 0.86 |
| 6q25.1 | (16) | rs2046210 | 151990059 | A/G | 0.48 | No | Genotyped | 0.77 | 1.00 (0.85,1.18) | 1.00 |
| 8q24.21 | (8) | rs13281615 | 128424800 | G/A | 0.44 | Yes | 0.9176 | 1.08 | 1.16 (0.99,1.37) | 0.072 |
| 9p21.3 | (15) | rs1011970 | 22052134 | G/T | 0.32 | Yes | 0.9398 | 1.09 | 1.07 (0.90,1.28) | 0.45 |
| 10p15.1 | (15) | rs2380205 | 5926740 | C/T | 0.49 | No | Genotyped | 0.94 | 0.98 (0.84,1.16) | 0.85 |
| 10q21.2 | (15) | rs10995190 | 63948688 | G/A | 0.16 | Yes | 0.9754 | 0.86 | 1.12 (0.89,1.41) | 0.33 |
| 10q26.13 | (10) | rs704010 | 80511154 | A/G | 0.19 | No | Genotyped | 0.93 | 1.11 (0.84,1.47) | 0.47 |
| 10q26.13 | (14, 15) | rs2981579 | 123327325 | G/A | 0.45 | Yes | 0.8214 | 1.17 | 0.99 (0.83,1.17) | 0.87 |
| 10q26.13 | (8) | rs1219648 | 123336180 | A/G | 0.41 | No | Genotyped | 1.20 | 1.17 (1.00,1.37) | 0.051 |
| 10p22.3 | (15) | rs2981582 | 123342307 | A/G | 0.45 | No | Genotyped | 1.26 | 0.93 (0.79,1.09) | 0.38 |
| 11q13.1 | (15) | rs3817198 | 1865582 | A/G | 0.19 | No | Genotyped | 1.07 | 1.10 (0.91,1.34) | 0.32 |
| 11p15.5 | (8) | rs614367 | 69037945 | A/G | 0.12 | No | Genotyped | 0.87 | 1.13 (0.89,1.44) | 0.30 |
| 14q24.1 | (14) | rs10483813 | 68101037 | T/A | 0.10 | Yes | 0.7915 | 1.06 | 1.05 (0.78, 1.42) | 0.76 |
| 16q12.1 | (8, 12, 14, 15) | rs3803662 | 51143842 | C/T | 0.47 | No | Genotyped | 1.30 | 0.79 (0.67,0.92) | 0.0034 |
| 16q12.1 | (11) | rs4784227 | 51156689 | C/T | 0.15 | No | Genotyped | 1.24 | 1.23 (0.94,1.61) | 0.13 |
| 17q23.2 | (7) | rs6504950 | 50411470 | G/A | 0.35 | Yes | 0.9930 | 0.95 | 1.06 (0.90, 1.26) | 0.47 |
1.
Listed as reference allele/tested allele.
2.
Minor allele frequency
3.
Imputation r2 is a measure of imputation quality from MACH
4.
ORs for discovery GWAS in this column are presented to have the same reference allele/tested allele as HR in this analysis (i.e. they are expressed in terms of the risk for the test allele compared to the reference allele. In some cases this required changing the reference allele from what was presented in the original presentation. All discovery GWAS had p-value <5×10−7.
5.
P-value from test of trend for each additional copy of the test allele.