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. Author manuscript; available in PMC: 2010 Sep 20.
Published in final edited form as: Nat Genet. 2009 May 17;41(6):724–728. doi: 10.1038/ng.385

Table 1.

SNPs showing the strongest associations (combined P value < 1×10-7) with age at menarche or age at natural menopause in joint analysis

SNP Cytological
Location		 Position a Nearby Genes b Major,
Minor
Alleles		 MAF c NHS
 WGHS
 Joint analysis
 Heterogeneity
Beta d S.E. P value e Beta d S.E. P value e Beta d, f S.E. P value e, f P value g
Age at Menarche
rs314277 6q21 105514355 LIN28B C, A 0.14 0.087 0.059 0.14 0.17 0.024 3.4E-13 0.16 0.022 2.7E-13 0.18
rs314263 6q21 105499438 LIN28B T, C 0.31 -0.0025 0.045 0.96 0.14 0.018 4.7E-15 0.12 0.017 3.2E-13 0.0037
rs369065 6q21 105550751 LIN28B T, C 0.33 0.00049 0.044 0.99 0.13 0.018 6.7E-13 0.11 0.016 2.4E-11 0.0078
rs7861820 9q31.2 106016229 T, C 0.48 -0.038 0.042 0.36 -0.099 0.016 2.1E-09 -0.090 0.015 3.4E-09 0.18
rs314280 6q21 105507530 LIN28B C, T 0.45 0.044 0.041 0.28 0.093 0.017 2.3E-08 0.086 0.015 2.3E-08 0.27
rs4946651 6q21 105476203 LIN28B G, A 0.45 0.044 0.041 0.29 0.092 0.017 3.0E-08 0.085 0.015 3.1E-08 0.27
rs12684013 9q31.2 106077669 C, T 0.27 -0.086 0.046 0.063 -0.096 0.019 2.1E-07 -0.095 0.017 3.6E-08 0.84
rs4452860 9q31.2 106004944 A, G 0.28 -0.082 0.045 0.072 -0.093 0.018 4.2E-07 -0.091 0.017 7.9E-08 0.83
rs7028916 9q31.2 106006623 C, A 0.28 -0.077 0.045 0.089 -0.093 0.018 4.1E-07 -0.090 0.017 9.7E-08 0.75
rs314262 6q21 105501314 LIN28B T, C 0.45 0.036 0.042 0.39 0.092 0.017 6.5E-08 0.084 0.016 9.7E-08 0.21
Age at Natural Menopause
rs16991615 20p12.3 5896227 TRMT6, MCM8 G, A 0.058 1.07 0.26 4.1E-05 1.07 0.12 7.6E-18 1.07 0.11 1.2E-21 1.00
rs1172822 19q13.42 60511657 BRSK1 C, T 0.37 -0.63 0.12 3.4E-07 -0.45 0.060 5.0E-14 -0.49 0.054 1.8E-19 0.19
rs2384687 19q13.42 60523000 BRSK1 T, C 0.39 -0.61 0.12 5.1E-07 -0.43 0.059 4.5E-13 -0.47 0.053 2.4E-18 0.18
rs897798 19q13.42 60525566 BRSK1, SUV420H2 A, G 0.47 -0.49 0.12 4.0E-05 -0.38 0.058 4.8E-11 -0.40 0.052 1.1E-14 0.42
rs365132 5q35.2 176311180 RAP80 G, T 0.49 0.43 0.12 0.00027 0.38 0.058 7.6E-11 0.39 0.052 8.4E-14 0.70
rs7718874 5q35.2 176290671 RAP80 A, G 0.49 0.43 0.12 0.00027 0.38 0.058 1.1E-10 0.39 0.052 1.3E-13 0.68
rs402511 5q35.2 176367046 RAP80, ZNF346 C, T 0.49 0.43 0.12 0.00028 0.38 0.058 1.2E-10 0.39 0.052 1.4E-13 0.69
rs7246479 19q13.42 60516144 BRSK1 G, T 0.48 0.45 0.12 0.00012 0.34 0.058 3.2E-09 0.36 0.052 2.3E-12 0.40
rs1551562 19q13.42 60506693 BRSK1 A, G 0.23 -0.69 0.14 8.8E-07 -0.37 0.069 8.4E-08 -0.43 0.062 2.6E-12 0.040
rs691141 5q35.2 176255904 HK3, RAP80 C, T 0.45 0.34 0.12 0.0039 0.37 0.058 2.9E-10 0.36 0.052 3.9E-12 0.85
rs12611091 19q13.42 60492141 HSPBP1, BRSK1 T, C 0.48 0.34 0.12 0.0043 0.32 0.059 4.5E-08 0.33 0.053 6.6E-10 0.88
rs2153157 6p24.2 11005474 GCM2, SYCP2L C, T 0.49 0.22 0.12 0.064 0.30 0.058 2.5E-07 0.29 0.052 5.1E-08 0.54
rs2278493 5q35.2 176247040 UNC5A, HK3 G, A 0.33 -0.27 0.12 0.031 -0.31 0.062 7.9E-07 -0.30 0.056 7.2E-08 0.77
a

Position based on NCBI genome build 35.

b

Genes within 20kb upstream and 10kb downstream of the SNP.

c

Minor allele frequency among combined sample of the NHS and the WGHS.

d

The regression parameter beta refers to the mean change in age at menarche or age at natural menopause in years per copy of the SNP minor allele.

e

P values are based on a trend test adjusted for the top principle components of genetic variation chosen for each study.

f

Combined effect sizes and P values are calculated using a fixed-effect meta-analysis.

g

P values for heterogeneity are calculated based on Q statistics with one degree of freedom.