Skip to main content

Table 3 Combination of FBAT and GEE, for grouped BMD phenotypes*

From: Genome-wide association with bone mass and geometry in the Framingham Heart Study

3a: Combination of FBAT and GEE, for grouped BMD phenotypes in men and women combined
Chrom Physical Position SNP Min p-value by GEE Min p-value by FBAT % Significant P-values by GEE & FBAT** Function Gene symbol
1 177,489,285 rs7544774 3.34 × 10-4 7.55 × 10-3 67 intron XPR1
1 231,181,475 rs7554650 1.67 × 10-4 5.93 × 10-3 67 unknown  
2 6,719,916 rs7584788 7.55 × 10-3 5.19 × 10-4 67 unknown  
2 15,963,228 rs2380707 1.14 × 10-3 5.22 × 10-4 67 unknown  
2 79,078,098 rs1261226 1.19 × 10-5 4.47 × 10-3 67 unknown  
4 177,742,191 rs9312601 2.22 × 10-3 7.03 × 10-4 67 unknown  
4 181,139,118 rs10520437 5.23 × 10-4 7.72 × 10-5 100 unknown  
4 181,162,903 rs922028 8.45 × 10-4 1.53 × 10-5 100 unknown  
5 26,917,842 rs1479679 1.13 × 10-4 2.38 × 10-4 67 intron CDH9
5 53,527,854 rs16882423 1.65 × 10-3 2.38 × 10-3 67 intron ARL15
7 9,739,152 rs1557978 1.73 × 10-4 3.97 × 10-4 33 intron  
7 11,301,740 rs10486135 1.67 × 10-4 5.95 × 10-4 67 intron  
7 18,183,021 rs10486301 1.94 × 10-4 9.43 × 10-4 67 unknown  
8 114,092,330 rs1156075 5.55 × 10-3 8.51 × 10-3 67 intron CSMD3
11 95,219,586 rs546809 1.41 × 10-3 7.10 × 10-5 67 intron MTMR2
12 103,526,872 rs10507180 7.18 × 10-4 4.16 × 10-3 100 intron CHST11
16 76,268,225 rs8051539 2.08 × 10-3 5.80 × 10-3 67 unknown  
18 48,132,968 rs768207 1.94 × 10-3 2.99 × 10-3 67 intron DCC
19 42,607,072 rs1465434 1.51 × 10-3 7.17 × 10-4 67 intron ZNF569
21 39,078,994 rs1209926 2.51 × 10-4 3.21 × 10-5 33 unknown C21orf24/ETS2
3b: Sex-specific results for grouped BMD phenotypes
Chrom Physical Position SNP Sex Min p-value by GEE Min p-value by FBAT Function Gene symbol
1 48,261,693 rs560004 Males 8.91 × 10-4 3.48 × 10-3 unknown  
1 200,641,877 rs1935588 Females 6.14 × 10-4 7.62 × 10-4 unknown  
2 125,809,045 rs1215318 Males 1.23 × 10-4 2.96 × 10-4 unknown  
4 181,162,903 rs922028 Females 1.61 × 10-4 6.16 × 10-3 unknown  
5 26,917,842 rs1479679 Females 4.36 × 10-5 6.96 × 10-3 intron CDH9
6 47,657,085 rs9296566 Females 2.27 × 10-4 5.08 × 10-4 intron CD2AP
6 83,666,784 rs9294266 Males 5.32 × 10-4 2.01 × 10-3 intron C6orf157
7 33,440,554 rs10486541 Males 1.54 × 10-5 1.95 × 10-3 unknown  
7 35,084,096 rs10486661 Females 9.34 × 10-6 9.98 × 10-5 unknown TBX20
9 20,592,188 rs7867710 Females 6.96 × 10-4 2.97 × 10-3 intron MLLT3
9 88,679,511 rs1779308 Males 3.09 × 10-3 4.94 × 10-3 unknown  
11 96,720,041 rs10501872 Females 4.03 × 10-4 1.02 × 10-3 unknown  
12 20,059,354 rs10505843 Females 2.02 × 10-4 7.38 × 10-3 unknown  
13 52,997,850 rs9316628 Females 2.51 × 10-3 5.22 × 10-4 unknown  
13 107,573,163 rs1223978 Males 3.42 × 10-4 5.07 × 10-4 unknown  
15 55,974,260 rs10518945 Females 6.19 × 10-5 6.15 × 10-4 unknown ALDH1A2
17 11,054,857 rs2024134 Males 4.75 × 10-3 6.31 × 10-5 unknown  
17 53,546,007 rs181224 Males 2.15 × 10-5 2.90 × 10-3 unknown Dlc2/OR4D1/OR4D2
18 48,132,968 rs768207 Females 1.35 × 10-4 2.57 × 10-4 intron DCC
20 18,310,297 rs2328293 Females 7.74 × 10-4 4.35 × 10-3 locus C20orf12
  1. * Femoral neck, Trochanter, Lumbar spine BMD
  2. ** Percentage of traits nominally significantly associated with the SNP at p < 0.01 in both GEE and FBAT
  3. Subsamples with N < 400 excluded.
  4. Percentage of traits nominally significantly associated at p < 0.01 in both GEE and FBAT was 67% for all SNPs.