    
MCBCS

SASBAC
 

Chr

Gene Name

Effect

SNP

Position (bp)

N

PMD
Est (SE)/
adj mean^{c}

Pvalue^{d}

N

Sqrt PMD Est (SE)/
adj mean^{e}

Pvalue^{d}

PHet^{f}


1

GALNT2

Ordinal

rs1043908

228483917

484

2.88 (1.28)

0.025

725

0.314 (0.135)

0.02

< 0.001

 
A/A
  
373

17.9
 
555

19.0
  
 
A/G
  
102

20.8
 
158

16.3
  
 
G/G
  
9

23.6
 
12

13.9
  
2

LOC375190

Ordinal

rs2080727

24204411

484

1.69 (0.85)

0.048

725

0.185 (0.095)

0.05

0.54

 
A/A
  
195

17.2
 
305

17.1
  
 
A/G
  
215

19.4
 
332

18.7
  
 
G/G
  
74

20.2
 
88

20.3
  
6

MCM3

Ordinal

rs3765447

52249471

483

3.62 (1.76)

0.040

725

0.45 (0.188)

0.017

0.96

 
A/A
  
422

18.2
 
644

17.7
  
 
A/G
  
60

22.3
 
76

21.7
  
 
G/G
  
1

12.7
 
5

26.1
  
8

TNKS

Ordinal

rs12549064

9479437

484

2.15 (1.09)

0.048

725

0.321 (0.116)

0.006

0.001

 
A/A
  
303

19.5
 
496

17.8
  
 
A/C
  
166

17.4
 
205

20.6
  
 
C/C
  
15

15.1
 
24

23.6
  
10

KIF11

Ordinal

rs2275220

94362686

484

4.23 (2.12)

0.046

726

0.45 (0.172)

0.009

0.005

 
A/A
  
448

19.0
 
613

17.9
  
 
A/G
  
34

13.5
 
111

22.0
  
 
G/G
  
2

20.4
 
2

26.4
  
11

STIM1

Ordinal

rs3794050

4068476

484

2.85 (1.38)

0.039

726

0.383 (0.142)

0.007

0.003

 
G/G
  
389

17.8
 
547

19.4
  
 
G/A
  
89

23.0
 
173

16.2
  
 
A/A
  
6

8.6
 
6

13.3
  
17

AURKB

Ordinal

rs3027260

8053911

484

3.33 (1.52)

0.029

726

0.404 (0.177)

0.022

0.73

 
G/G
  
404

19.2
 
632

18.7
  
 
G/A
  
77

15.8
 
91

15.4
  
 
A/A
  
3

12.8
 
3

12.4
  
 
Ordinal

rs4792590

8057840

484

3.14 (1.34)

0.020

726

0.39 (0.152)

0.010

0.89

 
G/G
  
377

19.3
 
597

18.6
  
 
G/A
  
102

16.6
 
121

15.4
  
 
A/A
  
5

9.5
 
8

12.5
  
 ^{a}P ≤ 0.05 in both studies. ^{b}Mayo Clinic Breast Cancer Study; Singapore and Sweden Breast Cancer Study.
 ^{c}PMD Est(SE): ordinal parameter estimate and standard error reflecting the estimated change in percent density per each additional copy of the minor allele carried. Adjusted mean from general model: least squares estimate of mean percent density for each genotype, adjusted for age, BMI, and PMH. ^{d}Pvalue from analyses adjusted for age, BMI, and PMH. ^{e}Sqrt PMD Est(SE): ordinal parameter estimate and standard error reflecting the estimated change in percent density error per each additional copy of the minor allele carried. Adjusted mean from general model: least squares estimate of mean percent density for each genotype, adjusted for age, BMI, and PMH. Least squares means back transformed from square root to original scale. ^{f}Pvalue from test for heterogeneity from metaanalysis performed on the ordinal parameter estimates (ordinal estimates for the MCBCS sample were estimated using square root transformed PMD).