Table 2.
Genomic loci associated with breast cancer (P-value < 10−5).
| SNP | Chr | Position (hg19) | Nearest Genes (distance to gene) | Function | Risk Allele (fwd) | RAF in 1 kG Phase3a | Korean BRCAX cases (initial) | Asian high-risk cases (replication) | Meta-analysis | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EAS | EUR | RAF in casesa | P-value | OR (95% CI)b | RAF in casesa | P-value | OR (95% CI)b | P-value | OR (95% CI)b | P hetero c | ||||||
| rs60538652 | 3 | 150473606 | SIAH2 | Intron | A | 0.61 | 0.98 | 0.65 | 6.24.E-07 | 1.26 (1.15–1.38) | 0.73 | 0.072 | 1.13 (0.99–1.28) | 3.25.E-07 | 1.21 (1.13–1.31) | 0.16 |
| rs11154838 | 6 | 136290942 | PDE7B | Intron | C | 0.72 | 0.65 | 0.75 | 1.28.E-06 | 1.27 (1.15–1.40) | 0.83 | 0.005 | 1.26 (1.07–1.49) | 2.27.E-08 | 1.27 (1.17–1.38) | 0.96 |
| rs9383936 | 6 | 151944614 | 3′ of CCDC170 (2.3 Kb), 5′ of ESR1 (3.3 Kb) | Intergenic | A | 0.31 | 0.08 | 0.34 | 1.01.E-10 | 1.35 (1.23–1.48) | 0.34 | 1.05.E-06 | 1.3 (1.17–1.44) | 6.35.E-16 | 1.33 (1.24–1.42) | 0.58 |
| rs10953105 | 7 | 93622247 | BET1 | 3′ UTR | G | 0.86 | 0.97 | 0.88 | 1.13.E-06 | 1.37 (1.21–1.56) | 0.91 | 0.192 | 1.14 (0.94–1.38) | 1.81.E-06 | 1.30 (1.16–1.44) | 0.11 |
| rs2350923 | 8 | 62605259 | ASPH | Intron | T | 0.72 | 0.70 | 0.76 | 7.75.E-07 | 1.28 (1.16–1.42) | 0.27 | 0.750 | 1.02 (0.92–1.13) | 0.250 | 1.14 (0.91–1.44) | 0.00 |
| rs78545330 | 9 | 21995941 | CDKN2B-AS1 | Intron | A | 0.21 | 0.08 | 0.26 | 3.41.E-06 | 1.26 (1.14–1.39) | 0.20 | 5.73.E-03 | 1.19 (1.05–1.35) | 8.56.E-08 | 1.23 (1.14–1.33) | 0.47 |
| rs10814070 | 9 | 34129839 | 3′ of DCAF12 (3.1 Kb) | Intergenic | T | 0.71 | 0.25 | 0.75 | 1.93.E-06 | 1.26 (1.15–1.39) | 0.65 | 0.469 | 0.96 (0.87–1.07) | 0.465 | 1.10 (0.85–1.44) | 0.00 |
| rs2912774 | 10 | 123348662 | FGFR2 | Intron | T | 0.38 | 0.43 | 0.42 | 5.96.E-07 | 1.25 (1.14–1.36) | 0.43 | 0.052 | 1.11 (1.00–1.21) | 5.60.E-07 | 1.18 (1.10–1.25) | 0.06 |
| rs9418690 | 10 | 128809949 | DOCK1 | Intron | C | 0.73 | 0.76 | 0.76 | 1.08.E-06 | 1.28 (1.16–1.41) | 0.82 | 0.819 | 1.02 (0.85–1.23) | 0.183 | 1.16 (0.93–1.44) | 0.04 |
| rs4964006 | 12 | 26770889 | ITPR2 | Intron | T | 0.95 | 0.69 | 0.98 | 1.52.E-06 | 1.96 (1.49–2.58) | 0.95 | 0.804 | 0.97 (0.76–1.24) | 0.366 | 1.38 (0.69–2.75) | 0.00 |
| rs67129489 | 12 | 96016957 | 5′ of PGAM1P5 (26.0 Kb), 5′ of NTN4 (34.6 Kb) | Intergenic | G | 0.13 | 0.32 | 0.15 | 9.31.E-07 | 1.36 (1.20–1.53) | 0.06 | 0.976 | 1.00 (0.77–1.32) | 0.226 | 1.20 (0.89–1.60) | 0.05 |
| rs278050 | 13 | 30436968 | 5′ of UBL3 (73 Kb) | Intergenic | C | 0.19 | 0.23 | 0.21 | 3.89.E-06 | 1.28 (1.15–1.42) | 0.19 | 0.050 | 1.13 (1.00–1.28) | 1.64.E-06 | 1.22 (1.12–1.32) | 0.14 |
| rs4784227 | 16 | 52583143 | TOX3 | Intron | T | 0.26 | 0.25 | 0.32 | 9.11.E-09 | 1.31 (1.19–1.44) | 0.29 | 6.24.E-05 | 1.25 (1.12–1.39) | 3.26.E-12 | 1.28 (1.20–1.38) | 0.49 |
| rs4969001 | 17 | 70980127 | SLC39A11 | Intron | T | 0.89 | 0.96 | 0.86 | 6.53.E-06 | 1.32 (1.17–1.49) | 0.89 | 0.041 | 0.85 (0.73–0.99) | 0.780 | 1.06 (0.69–1.64) | 0.00 |
| rs73107564 | 20 | 36263775 | — | Intergenic | A | 0.89 | 0.81 | 0.89 | 1.81.E-07 | 1.43 (1.25–1.63) | 0.87 | 0.541 | 0.96 (0.83–1.10) | 0.432 | 1.17 (0.79–1.73) | 0.00 |
aRAF: risk allele frequency, EAS: East Asian, EUR: European.
bOR: odds ratio, CI: confidence interval.
cPhetero: P-value for heterogeneity. Fixed effect model was used if p-value for heterogeneity exceeds 0.05; otherwise random effect model was used.