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. 2013 Nov 10;179(3):382–394. doi: 10.1093/aje/kwt258

Table 3.

Comparison of Odds Ratios and Confidence Limit Ratios or Posterior Limit Ratios for Frequentist, Basic Hierarchical, and Bayesian Regression Models Among African American Women (766 Cases and 681 Controls) in the Carolina Breast Cancer Study, North Carolina, 1993–2001

Locus and LD Block SNP Reference No. Reference
 Model Type
MLE
 Bayesian
 Hierarchical
ORa 95% CI ORb 95% CI CLR ORb 95% PI PLR ORc 95% PI PLR
1p12 rs11249433d 28 1.14 1.10, 1.19 1.26 0.99, 1.60 1.61 1.22 0.96, 1.48 1.53 1.26 0.99, 1.60 1.61
CASP8 block 1 rs1045485e 33 1.12 1.08, 1.18 0.93 0.67, 1.29 1.93 0.96 0.69, 1.22 1.77 1.12 0.39, 3.17 8.05
CASP8 block 1 rs17468277 1.09 0.78, 1.54 1.99 1.07 0.78, 1.38 1.78 1.20 0.41, 3.53 8.68
2q35 rs13387042d 27 1.20 1.14, 1.26 1.02 0.86, 1.22 1.43 1.02 0.86, 1.20 1.39 1.02 0.86, 1.22 1.43
2p rs4666451f 23 1.03 1.00, 1.06 1.15 0.96, 1.39 1.45 1.13 0.95, 1.34 1.41 1.15 0.96, 1.39 1.45
SLC4A7 rs4973768d 29 1.16 1.10, 1.24 0.90 0.77, 1.06 1.38 0.91 0.77, 1.04 1.35 0.90 0.77, 1.06 1.38
4p rs12505080f 25 1.15g 1.03, 1.28 1.09 0.88, 1.34 1.52 1.08 0.88, 1.30 1.48 1.09 0.88, 1.34 1.52
TLR1 rs7696175f 25 1.12g 1.00, 1.26 1.39 1.04, 1.86 1.79 1.29 0.99, 1.66 1.68 1.39 1.04, 1.86 1.80
MRPS30 rs4415084d 32 1.16 1.10, 1.21 1.13 0.97, 1.33 1.38 1.13 0.96, 1.30 1.35 1.13 0.97, 1.33 1.38
MRPS30 rs10941679f 32 1.19 1.13, 1.26 1.00 0.82, 1.22 1.49 1.01 0.83, 1.19 1.43 1.00 0.82, 1.22 1.49
5p12 rs981782d 23 1.04 1.01, 1.08 1.11 0.84, 1.46 1.74 1.09 0.84, 1.36 1.61 1.11 0.84, 1.46 1.74
5q rs30099f 23 1.05 1.01, 1.10 1.22 0.98, 1.52 1.55 1.19 0.96, 1.44 1.50 1.22 0.98, 1.52 1.55
MAP3K1 rs889312d 23 1.13 1.10, 1.16 0.95 0.80, 1.13 1.41 0.96 0.81, 1.11 1.37 0.95 0.80, 1.13 1.41
ESR1 rs2046210d 30 1.29 1.21, 1.37 1.22 1.04, 1.43 1.38 1.20 1.03, 1.39 1.35 1.22 1.04, 1.43 1.38
ESR1 rs851974 0.93 0.76, 1.14 1.50 0.94 0.78, 1.13 1.45 0.93 0.75, 1.14 1.50
ESR1 rs2077647 1.07 0.92, 1.25 1.37 1.07 0.92, 1.23 1.34 1.07 0.92, 1.25 1.37
ESR1 rs2234693 0.96 0.82, 1.13 1.37 0.97 0.83, 1.12 1.35 0.96 0.82, 1.13 1.37
ESR1 rs1801132e 33 1.05 1.00, 1.11 1.19 0.93, 1.52 1.64 1.16 0.91, 1.42 1.55 1.19 0.93, 1.52 1.64
ESR1 rs3020314e 33 1.12 1.06,1.18 1.00 0.84, 1.19 1.41 1.01 0.85, 1.17 1.37 1.00 0.84, 1.19 1.41
ESR1 rs3798577 1.02 0.88, 1.19 1.36 1.02 0.89, 1.18 1.33 1.02 0.87, 1.19 1.36
ECHDC1 rs2180341d 24 1.41 1.25, 1.59 0.98 0.83, 1.15 1.39 0.98 0.84, 1.14 1.36 0.98 0.83, 1.15 1.39
RELN rs17157903f 25 1.11 1.00, 1.23 1.07 0.83, 1.37 1.64 1.07 0.85, 1.31 1.54 1.07 0.83, 1.37 1.64
8q24 rs13281615d 23 1.08 1.05, 1.11 1.00 0.86, 1.18 1.38 1.01 0.85, 1.17 1.37 1.00 0.86, 1.18 1.38
8q24 rs1562430d 29 1.17 1.10, 1.25 1.00 0.86, 1.17 1.36 1.00 0.87, 1.16 1.34 1.00 0.86, 1.17 1.36
CDKN2A/B rs3731257 0.88 0.67, 1.15 1.71 0.91 0.71, 1.14 1.60 0.88 0.67, 1.15 1.71
CDKN2A/B block 1 rs518394 1.01 0.76, 1.35 1.76 1.02 0.78, 1.28 1.64 1.01 0.73, 1.40 1.76
CDKN2A/B block 1 rs564398 1.01 0.75, 1.35 1.79 1.01 0.77, 1.27 1.66 1.00 0.72, 1.40 1.96
CDKN2A/B rs1011970d 29 1.20 1.11, 1.30 0.95 0.81, 1.11 1.38 0.96 0.82, 1.10 1.34 0.95 0.81, 1.11 1.38
CDKN2A/B rs10757278 0.91 0.75, 1.12 1.50 0.93 0.76, 1.09 1.44 0.91 0.75, 1.12 1.50
CDKN2A/B rs10811661 1.00 0.74, 1.35 1.83 1.01 0.76, 1.28 1.67 1.00 0.74, 1.35 1.83
ANKRD16 rs2380205d 29 1.06 1.02, 1.10 0.97 0.83, 1.13 1.37 0.98 0.84, 1.13 1.34 0.97 0.83, 1.13 1.37
ZNF365 rs10995190d 29 1.16 1.10, 1.22 1.06 0.87, 1.29 1.49 1.05 0.86, 1.23 1.44 1.06 0.87, 1.29 1.49
ZMIZ1 rs704010d 29 1.07 1.03, 1.11 1.05 0.80, 1.36 1.69 1.04 0.80, 1.28 1.61 1.05 0.80, 1.36 1.69
FGFR2 rs1896395 1.01 0.83, 1.23 1.48 1.02 0.84, 1.20 1.44 1.01 0.83, 1.23 1.48
FGFR2 block 1 rs3750817 1.74 1.34, 2.26 1.69 1.61 1.22, 2.02 1.66 1.38 1.05, 1.83 1.74
FGFR2 block 1 rs10736303f 23 1.25 1.18, 1.32 1.39 1.12, 1.74 1.56 1.33 1.07, 1.61 1.51 1.08 0.83, 1.39 1.67
FGFR2 block 1 rs11200014 1.04 0.86, 1.26 1.47 1.04 0.85, 1.23 1.45 0.97 0.70, 1.34 1.92
FGFR2 block 1 rs2981579d 28 1.17g 1.07, 1.27 1.22 1.04, 1.42 1.36 1.19 1.03, 1.37 1.33 1.10 0.93, 1.31 1.41
FGFR2 block 1 rs1078806f 24 1.26 1.13, 1.40 1.06 0.88, 1.29 1.47 1.06 0.87, 1.25 1.43 1.00 0.72, 1.38 1.92
FGFR2 block 2 rs2981578f 23 1.26 1.19, 1.34 1.42 1.14, 1.77 1.56 1.36 1.10, 1.65 1.51 1.23 0.99, 1.53 1.54
FGFR2 block 2 rs1219648d 25 1.27 1.18, 1.36 1.19 1.02, 1.39 1.37 1.18 1.01, 1.35 1.33 1.01 0.82, 1.24 1.51
FGFR2 block 2 rs2912774f 23 1.26 1.19, 1.34 1.27 1.09, 1.49 1.37 1.25 1.06, 1.43 1.35 1.09 0.80, 1.49 1.85
FGFR2 block 2 rs2936870f 23 1.26 1.19, 1.34 1.27 1.09, 1.48 1.37 1.25 1.07, 1.44 1.34 1.09 0.80, 1.48 1.84
FGFR2 block 3 rs2420946f 25 1.25 1.18, 1.36 1.17 1.00, 1.37 1.37 1.16 1.00, 1.35 1.35 0.95 0.72, 1.25 1.73
FGFR2 block 3 rs2162540 1.23 1.05, 1.44 1.36 1.21 1.04, 1.40 1.34 1.27 0.96, 1.66 1.37
FGFR2 rs2981582d 23 1.26 1.23, 1.30 1.19 1.02, 1.39 1.37 1.18 1.00, 1.35 1.35 1.19 1.02, 1.39 1.37
FGFR2 rs3135718f 23 1.15 1.07, 1.23 1.26 1.08, 1.46 1.35 1.24 1.07, 1.43 1.33 1.26 1.08, 1.46 1.35
10q rs10510126f 25 1.20 1.08, 1.35 1.04 0.82, 1.32 1.61 1.04 0.82, 1.25 1.53 1.04 0.82, 1.32 1.61
ATM rs1801516 1.22 0.77, 1.95 2.54 1.14 0.76, 1.58 2.08 1.22 0.77, 1.95 2.54
ATM rs664143 0.95 0.81, 1.11 1.38 0.96 0.82, 1.10 1.35 0.95 0.81, 1.11 1.38
ATM rs170548 0.86 0.67, 1.11 1.66 0.90 0.70, 1.10 1.57 0.86 0.67, 1.11 1.66
ATM rs3092993 1.22 0.77, 1.95 2.54 1.14 0.76, 1.58 2.08 1.22 0.77, 1.95 2.54
LSP1 rs3817198d 23 1.07 1.04, 1.11 1.01 0.82, 1.24 1.52 1.01 0.84, 1.21 1.47 1.01 0.82, 1.24 1.52
LSP1 rs909116d 29 1.17 1.10, 1.24 1.00 0.84, 1.19 1.42 1.01 0.84, 1.17 1.39 1.00 0.84, 1.19 1.42
H19 rs2107425f 23 1.04 1.01, 1.08 0.84 0.71, 0.98 1.38 0.86 0.73, 0.98 1.35 0.84 0.71, 0.98 1.38
TOX3 rs8049149 0.92 0.54, 1.56 2.87 0.98 0.64, 1.35 2.10 0.92 0.54, 1.56 2.87
TOX3 rs16951186 0.90 0.74, 1.09 1.49 0.92 0.76, 1.10 1.45 0.90 0.74, 1.09 1.49
TOX3 rs8051542f 23 1.09 1.06, 1.13 1.14 0.97, 1.35 1.39 1.13 0.97, 1.30 1.35 1.14 0.97, 1.35 1.39
TOX3 rs12443621f 23 1.11 1.08, 1.14 0.86 0.74, 1.01 1.36 0.88 0.75, 1.00 1.34 0.86 0.74, 1.01 1.36
TOX3 block 1 rs3803662d 23 1.20 1.16, 1.24 1.06 0.90, 1.23 1.37 1.05 0.91, 1.21 1.34 1.11 0.94, 1.31 1.39
TOX3 block 1 rs4784227d 26 1.25 1.20, 1.31 1.25 0.93, 1.67 1.80 1.19 0.90, 1.51 1.67 1.28 0.96, 1.71 1.77
TOX3 block 2 rs3104746 1.54 1.27, 1.86 1.46 1.49 1.22, 1.75 1.43 1.39 1.14, 1.71 1.50
TOX3 block 2 rs3112562 1.28 1.09, 1.50 1.37 1.26 1.09, 1.46 1.35 1.12 0.94, 1.33 1.41
TOX3 rs9940048 1.10 0.93, 1.31 1.40 1.10 0.92, 1.29 1.39 1.10 0.93, 1.31 1.41
TP53 rs9894946 0.96 0.68, 1.36 2.01 0.98 0.70, 1.28 1.82 0.96 0.68, 1.37 2.01
TP53 rs1614984 1.07 0.92, 1.25 1.36 1.07 0.91, 1.22 1.34 1.07 0.92, 1.25 1.36
TP53 block 1 rs12951053e 33 1.15 1.04, 1.26 1.03 0.80, 1.32 1.64 1.03 0.81, 1.25 1.55 1.01 0.77, 1.32 1.71
TP53 block 1 rs2909430 1.06 0.89, 1.25 1.40 1.06 0.89, 1.22 1.37 1.04 0.84, 1.28 1.52
TP53 block 1 rs1042522 0.98 0.83, 1.15 1.38 0.98 0.83, 1.13 1.36 1.00 0.82, 1.22 1.50
TP53 rs8079544 0.89 0.69, 1.15 1.66 0.92 0.72, 1.12 1.57 0.89 0.69, 1.15 1.66
COX11 block 1 rs7222197f 29 1.12 1.04, 1.20 1.14 0.97, 1.33 1.38 1.12 0.95, 1.29 1.36 1.07 0.77, 1.47 1.90
COX11 block 1 rs6504950f 31 1.05 1.03, 1.09 1.13 0.96, 1.32 1.37 1.12 0.95, 1.28 1.35 1.07 0.77, 1.47 1.90

Abbreviations: CI, confidence interval; CLR, confidence limit ratio; GWAS, genome-wide association study; LD, linkage disequilibrium; MLE, maximum likelihood estimated; OR, odds ratio; PI, posterior interval; PLR, posterior limit ratio; SNP, single nucleotide polymorphism.

a Odds ratios from initial GWAS or candidate gene meta-analyses (if met criteria for cumulative evidence of association); all odds ratios for log-additive genetic models, unless otherwise specified. Those without values are not GWAS hits and were not included in the candidate gene meta-analysis.

b Adjusted for age at diagnosis (cases) or selection (controls) and proportion of African ancestry.

c Adjusted for age at diagnosis (cases) or selection (controls), proportion of African ancestry, and other SNPs in the LD block.

d Previous GWAS hit.

e Cumulative evidence of an association in the meta-analysis by Zhang et al. (40).

f Other GWAS-identified gene.

g Odds ratio estimated using general genetic model.