Table 1.
Results for the 15 regions with combined P<5×10−8. Results are shown for the strongest associated variant in the region.
| Best variant | Locus | Position2 | Alleles3 | EAF4 | r25 | GWAS OR (95% CI)6 |
GWAS P7 | iCOGS OR (95% CI) |
iCOGS P | Combined GWAS + iCOGS P |
Genes within +/−2kb |
Enhancers in MCF7/HMEC |
eQTLs |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs12405132 | 1q21.1 | 145644984 | C/T | 0.36 | 0.96 | 0.96 (0.92–0.99) | 0.00962 | 0.95 (0.93–0.97) | 2.34×10−7 | 7.92×10−9 | LOC10028814, NBPF10, RNF115 | RNF115, POLR3C,PDZK1, PIAS3 | - |
| rs12048493 | 1q21.2 | 149927034 | A/C | 0.34 | 0.76 | 1.04 (0.99–1.09) | 0.121 | 1.07 (1.05–1.10) | 1.66×10−9 | 1.10×10−9 | - | - | - |
| rs72755295 | 1q43 | 242034263 | A/G | 0.03 | 0.94 | 1.19 (1.03–1.39) | 0.021 | 1.15 (1.09–1.22) | 2.60×10−7 | 1.82×10−8 | EXO1 | - | - |
| rs6796502 | 3p21.3 | 46866866 | G/A | 0.09 | 0.91 | 0.92 (0.87–0.98) | 0.00657 | 0.92 (0.89–0.95) | 8.13×10−7 | 1.84×10−8 | - | - | - |
| rs13162653 | 5p15.1 | 16187528 | G/T | 0.45 | 0.72 | 0.92 (0.88–0.95) | 5.18×10−6 | 0.95 (0.93–0.97) | 1.71×10−6 | 1.08×10−10 | - | - | - |
| rs2012709 | 5p13.3 | 32567732 | C/T | 0.46 | 0.81 | 1.06 (1.02–1.09) | 0.00101 | 1.05 (1.03–1.08) | 1.66×10−6 | 6.38×10−9 | - | - | - |
| rs7707921 | 5q14 | 81538046 | A/T | 0.23 | 0.88 | 0.94 (0.9–0.98) | 0.00302 | 0.93 (0.91–0.95) | 4.09×10−9 | 5.00×10−11 | ATG10 | - | RPS23, ATP6AP1L |
| rs9257408 | 6p22.1 | 28926220 | G/C | 0.38 | 0.92 | 1.05 (1–1.1) | 0.0372 | 1.05 (1.03–1.08) | 4.53×10−7 | 4.84×10−8 | - | - | - |
| rs4593472 | 7q32.3 | 130667121 | C/T | 0.35 | 1.00 | 0.92 (0.88–0.96) | 2.57×10−5 | 0.95 (0.94–0.97) | 3.97×10−6 | 1.83×10−9 | FLJ43663 | - | - |
| rs13365225 | 8p11.23 | 36858483 | A/G | 0.17 | 0.94 | 0.89 (0.85–0.93) | 6.32×10−7 | 0.95 (0.93–0.98) | 0.000159 | 1.06×10−8 | - | - | - |
| rs13267382 | 8q23.3 | 117209548 | G/A | 0.36 | 0.97 | 1.07 (1.03–1.12) | 0.000537 | 1.05 (1.03–1.07) | 4.87×10−6 | 1.72×10−8 | LINC00536 | - | - |
| rs11627032 | 14q32.12 | 93104072 | T/C | 0.26 | 0.73 | 0.94 (0.9–0.98) | 0.00114 | 0.94 (0.92–0.96) | 1.06×10−6 | 4.48×10−9 | RIN3 | - | - |
| chr17:29230520 | 17q11.2 | 29230520 | GGT/G | 0.20 | 0.77 | 0.94 (0.89–0.98) | 0.009 | 0.93 (0.91–0.96) | 1.11×10−6 | 3.34×10−8 | ATAD5 | - | - |
| rs745570 | 17q25.3 | 77781725 | A/G | 0.50 | 0.93 | 0.94 (0.91–0.98) | 0.000754 | 0.95 (0.93–0.97) | 4.52×10−7 | 1.40×10−9 | - | - | - |
| rs6507583 | 18q12.3 | 42399590 | A/G | 0.07 | 0.96 | 0.91 (0.85–0.98) | 0.00803 | 0.91 (0.88–0.95) | 1.21×10−6 | 3.20×10−8 | SETBP1 | SETBP1 | - |
1
Chromosome
2
Build 37 position
3
Reference/effect allele, based on the forward strand
4
Mean effect allele frequency over all controls
5
Imputation r2 in the iCOGS samples (calculated by the average info score from IMPUTEv2)
6
Per allele odds ratio for the minor allele relative to the major allele
7
P value for the 1df trend test