|
Region
|
Index SNP (locus)
|
Chromosome
|
Length (Mbp)
|
SNV MAF ≤0.005
|
SNV MAF >0.005
|
High-impact SNVsb
|
p value (index SNP)
|
p value (top SNP)
|
Conditional analysis on top SNP p value (top SNP)
|
Conditional analysis on index SNP p value (top SNP)
|
|---|
|
1
|
rs13387042 (2q35)
|
2
|
0.122
|
3469
|
674
|
0
|
0.00016
|
2.68E-05 (rs6721996)
|
0.0070 (rs116670542)
|
0.0066 (rs116670542)
|
|
2
|
rs10069690 (TERT)
|
5
|
0.046
|
1681
|
167
|
0
|
0.0044
|
0.0044 (rs10069690)
|
0.025 (rs34768248)
|
0.025 (rs34768248)
|
|
3
|
rs889312 (MAP3K1)
|
5
|
0.308
|
6663
|
986
|
4
|
0.098
|
0.00035 (rs111944656)
|
0.0022 (rs79128470)
|
0.0021 (rs111944656)
|
|
4
|
rs2046210a (ESR1)
|
6
|
0.243
|
4209
|
727
|
10
|
0.015
|
0.00023 (rs9383938)
|
0.0074 (rs80347946)
|
0.0077 (rs80347946)
|
|
5
|
rs1562430 (8q24)
|
8
|
0.973
|
20,730
|
3260
|
5
|
0.18
|
9.87E-05 (rs112613843)
|
0.00020 (rs4871810)
|
0.00019 (rs4871841)
|
|
6
|
rs10995190 (ZNF365)
|
10
|
0.876
|
7635
|
1056
|
1
|
0.76
|
2.7E-05 (rs12570941)
|
0.0085 (rs73282644)
|
5.39E-05 (rs12570941)
|
|
7
|
rs704010 (ZMIZ1)
|
10
|
0.398
|
13,622
|
1822
|
4
|
0.019
|
0.00025 (Chr10-81107117)
|
0.00076 (rs117770051)
|
0.00019 (Chr10-81107117)
|
|
8
|
rs2981579 (FGFR2)
|
10
|
0.473
|
20,081
|
3033
|
15
|
0.00046
|
4.42E-05 (rs10736303)
|
0.00020 (rs192776427)
|
0.00024 (rs192776427)
|
|
9
|
rs614367 (11q13)
|
11
|
0.259
|
6743
|
1010
|
5
|
0.75
|
2.15E-06 (rs61041893)
|
0.00032 (rs11823311)
|
5.47E-05 (rs598003)
|
|
10
|
rs999737 (RAD51B)
|
14
|
0.815
|
15,992
|
2025
|
8
|
0.067
|
0.00050 (rs76904544)
|
0.00086 (rs113627141)
|
0.00074 (rs113627141)
|
|
11
|
rs3803662 (TOX3)
|
16
|
0.269
|
7337
|
910
|
0
|
0.036
|
0.00013 (rs12922061)
|
0.0013 (rs8048809)
|
0.0013 (rs4784227)
|
|
12
|
rs8170 (MERIT40)
|
19
|
0.712
|
13,080
|
1880
|
31
|
0.67
|
0.0035 (rs62126223)
|
0.0069 (rs117673644)
|
0.0035 (rs62126223)
|
-
MAF Minor allele frequency, SNP Single-nucleotide polymorphism, SNV Single-nucleotide variant
- The results shown are derived from genome-wide association study index single-nucleotide polymorphisms and best associated single-nucleotide variant in sequenced regions spanning 12 breast cancer genome-wide association study loci. Results are also shown for conditional analysis adjusted for either best associated (“top”) SNP or the original index genome-wide association study SNP
-
aSNP was filtered in quality control, p value for rs12662670
-
bAs defined by SnpEff [43]
