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. Author manuscript; available in PMC: 2010 May 1.
Published in final edited form as: Nat Genet. 2009 Oct 4;41(11):1199–1206. doi: 10.1038/ng.446

Table 1.

Top genome-wide significant markers of the 20 loci associated at GWS with lumbar spine and/or femoral neck BMD

Marker Information
 Lumbar spine BMD
 Femoral neck BMD
Effect estimate (in SD)
 Heterogeneity
 Effect estimate (in SD)
 Heterogeneity
 Site
Specificity
Ho:βLS=βFN
Locus
 SNP
 A1*/A2
 FREQ*
 Type
 Closest
Gene
 Distance
(kb)
 Beta (?LS)
 SE
 P-value
 OMA-GC
P-value
 Q P-value
 I2
 Beta
 SE
 P-value
 OMA-GC
P-value
 Q P-value
 I2
 P-value
Novel loci associated with BMD at GWS level
1p31.3 rs1430742 T/C 0.79 I GPR177 44.0 0.105 0.014 2.6E-13 2.5E-12 0.26 21 0.100 0.014 1.8E-12 1.2E-11 0.75 0 0.82
rs2566755 T/C 0.79 G GPR177 44.3 0.104 0.014 3.3E-13 3.1E-12 0.27 20 0.100 0.014 1.7E-12 1.1E-11 0.76 0 0.83
3p22 rs87938 A/G 0.45 G CTNNB1 103.3 −0.043 0.012 1.7E-04 3.1E-04 0.24 23 −0.070 0.011 8.1E-10 3.4E-09 0.14 34.5 0.10
5q14 rs1366594 A/C 0.55 G MEF2C 197.0 0.005 0.012 0.65 0.66 NC NC −0.085 0.011 1.3E-13 1.1E-12 0.62 0 3.2E-08
7p14 rs1524058 T/C 0.40 I STARD3NL 81.7 −0.070 0.012 1.1E-09 5.2E-09 0.18 30 −0.038 0.011 8.9E-04 1.4E-03 0.05 48 0.05
7q21.3 rs4729260 C/G 0.68 I FLJ42280 14.9 −0.081 0.013 1.7E-10 9.5E-10 0.14 35 −0.085 0.012 9.4E-12 5.4E-11 0.77 0 0.82
rs7781370 T/C 0.34 I FLJ42280 0.7 −0.074 0.012 1.1E-09 5.5E-09 0.12 37 −0.083 0.012 4.7E-12 2.9E-11 0.68 0 0.60
11p14.1 rs16921914 A/G 0.27 G DCDC5 61.6 0.077 0.013 2.3E-09 1.0E-08 0.52 0 0.038 0.013 0.003 0.005 NC NC 0.03
11p15 rs7117858 A/G 0.80 G SOX6 297.3 −0.042 0.014 0.004 0.005 NC NC 0.088 0.014 6.4E-10 2.7E-09 0.70 0 1.5E-10
16q24 rs10048146 A/G 0.81 G FOXL1 95.4 −0.093 0.016 1.7E-08 6.0E-08 0.21 28 −0.085 0.016 1.7E-07 4.9E-07 0.96 0 0.73
17q12 rs9303521 T/G 0.46 G CRHR1 56.5 −0.068 0.012 1.4E-08 5.0E-08 0.05 49 −0.055 0.012 3.6E-06 8.3E-06 0.07 45 0.46
Suggestive loci now associated with BMD at GWS level
2p21 rs11898505 A/G 0.34 G SPTBN1 1.1 0.067 0.012 1.6E-08 6.3E-08 0.39 6 0.027 0.012 0.02 0.03 NC NC 0.02
4q21.1 rs1471403 T/C 0.34 G MEPE 7.3 0.068 0.012 1.5E-08 5.7E-08 0.18 30 0.059 0.012 7.8E-07 2.0E-06 0.56 0 0.58
11p11.2 rs7932354 T/C 0.29 I ARHGAP1 0.1 0.056 0.013 1.1E-05 2.4E-05 0.61 0 0.073 0.012 4.0E-09 1.5E-08 0.68 0 0.32
17q21 rs228769 C/G 0.80 I HDAC5 7.8 0.067 0.014 4.0E-06 1.0E-05 0.87 0 0.081 0.014 1.7E-08 5.8E-08 0.94 0 0.49
Known loci associated with BMD at GWS level
1p36 rs7524102 A/G 0.83 G ZBTB40 79.9 0.094 0.015 3.2E-10 1.7E-09 0.27 19.5 0.079 0.015 8.8E-08 2.6E-07 0.64 0 0.48
rs6426749 C/G 0.17 I ZBTB40 66.9 0.107 0.017 7.6E-10 3.8E-09 0.74 0 0.082 0.015 4.8E-08 1.5E-07 0.64 0 0.26
6q25 rs2504063 A/G 0.40 G ESR1 38.0 −0.078 0.012 6.1E-11 3.7E-10 0.03 52.7 −0.066 0.012 3.0E-08 9.6E-08 0.84 0 0.45
rs2941740 A/G 0.57 I C6orf97 67.3 0.070 0.012 2.0E-09 9.3E-09 0.01 59.0 0.073 0.012 2.0E-10 9.1E-10 0.02 57.2 0.84
8q24 rs2062377 A/T 0.56 I TNFRSF11B 43.0 0.094 0.012 3.5E-16 5.7E-15 0.31 15.4 0.062 0.011 5.4E-08 1.7E-07 0.61 0 0.05
rs11995824 C/G 0.45 I TNFRSF11B 48.3 −0.093 0.012 1.1E-15 1.6E-14 0.24 22.3 −0.066 0.011 7.1E-09 2.6E-08 0.48 0 0.10
11q13.4 rs599083 T/G 0.69 G LRP5 24.4 −0.067 0.012 4.7E-08 1.7E-07 0.50 0 −0.047 0.012 9.7E-05 0.0002 0.76 0 0.25
12q13 rs2016266 A/G 0.68 G SP7 1.6 0.070 0.012 1.3E-08 5.2E-08 0.93 0 0.046 0.012 1.9E-04 0.0003 0.81 0 0.16
13q14 rs9533090 T/C 0.50 I AKAP11 54.0 −0.120 0.012 5.4E-25 4.6E-23 0.02 57.1 −0.041 0.011 3.9E-04 0.0006 0.39 5.7 1.1E-06
18q21 rs884205 A/C 0.27 I TNFRSF11A 1.4 −0.078 0.0136 9.4E-09 3.8E-08 0.90 0 −0.039 0.013 0.004 0.005 NC NC 0.04

TypeSNP:G=Genotyped(atleastin1 study) I=Imputed

Distance: to coding region

Bold: P<5×10−8

OMA-GC: overall meta-analysis genomic control

NC: Not calculated P>0.001

Q P-value: Q-statistic P-value