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Table 2 Top genetic associations with bone density and geometry based on the lowest p-value for GEE test (2a), FBAT (2b), and Linkage (2c) analyses

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

2a: Top 25 associations with bone density and geometry based on the lowest p-value of the GEE test
Phenotype SNP Chrom. Physical Position GEE p-value FBAT p-value Gene region*
NeckZ1rf rs6600671 1 120,812,532 5.85 × 10 -7 3.18 × 10-3  
NeckZ1 rs2053506 3 19,350,795 3.74 × 10 -6 2.68 × 10-2 KCNH8
TRBMDm rs10510628 3 29,828,407 2.83 × 10 -6 2.91 × 10-2 RBMS3
NeckW1rf rs2054989 3 56,505,749 6.06 × 10 -7 2.36 × 10-3 ERC2
ShaftW1f rs922948 3 69,525,327 1.75 × 10 -6 3.47 × 10-3  
ShaftW1 rs991258 3 103,256,733 5.32 × 10 -7 3.12 × 10-2  
BUA rs9291683 4 10,000,429 2.07 × 10 -6 7.44 × 10-4  
NeckZ1rf rs2548003 5 28,783,080 2.40 × 10 -7 1.30 × 10-1  
NeckZ1rf rs10515148 5 71,752,684 6.10 × 10 -7 5.97 × 10-3 ZNF366
LSBMDf rs10514345 5 90,460,035 2.15 × 10 -6 9.85 × 10-2 GPR98
NeckZ1 Same as above    1.81 × 10 -7 3.03 × 10-2  
NeckW1rf rs4715166 6 13,324,037 2.69 × 10 -6 9.97 × 10-3 PHACTR1
BUA rs2214681 7 147,140,340 2.72 × 10 -6 2.26 × 10-2 CNTNAP2
ShaftZ1R rs10503887 8 31,752,989 2.23 × 10 -7 1.77 × 10-3 NRG1
FNBMDm rs2165468 10 3,506,105 1.07 × 10 -6 6.71 × 10-2  
ShaftW1f rs1452928 11 84,499,969 7.10 × 10 -7 7.43 × 10-3  
NeckZ1rf rs638882 11 115,269,255 3.50 × 10 -6 6.33 × 10-3  
ShaftZ1rf rs10492096 12 6,450,843 3.35 × 10 -6 2.17 × 10-3 VAMP1
TRBMD rs10506701 12 72,872,477 1.40 × 10 -6 1.25 × 10-1  
ShaftW1f rs10506821 12 78,999,391 2.03 × 10 -7 1.80 × 10-1  
NeckZ1rm rs1590305 13 36,933,189 3.15 × 10 -6 2.21 × 10-2  
FNBMDm rs9317284 13 62,532,351 2.44 × 10 -7 2.86 × 10-1  
TRBMDf rs4087296 16 80,935,282 3.11 × 10 -7 6.18 × 10-3  
NSAm rs4131805 18 24,313,110 2.07 × 10 -6 1.87 × 10-3  
TRBMDf rs4811196 20 35,903,108 1.13 × 10 -6 7.03 × 10-4 CTNNBL1
2b: Top 25 associations with bone density and geometry based on the lowest p value of the FBAT test
Phenotype SNP Chrom. Physical Position GEE p-value FBAT p-value Gene region
NeckW1rf rs1395548 1 162,045,085 2.34 × 10-3 1.22 × 10 -6 LMX1A
FNBMD rs1538173 1 165,373,720 6.77 × 10-2 2.80 × 10 -6 DPT
TRBMD rs3762397 1 196,821,876 5.96 × 10-3 2.78 × 10 -7 NR5A2
ShaftZ1rf rs9287234 1 236,892,414 9.71\ × 10-3 7.90 × 10 -6 FMN2
TRBMD rs914951 1 239,278,119 1.82 × 10-2 8.79 × 10 -6  
NeckW1 rs4143244 3 5,385,364 1.07 × 10-2 7.05 × 10 -7  
NeckW1rf rs1349205 3 54,093,157 2.22 × 10-2 1.42 × 10 -5 CACNA2D3
ShaftW1 rs1870007 3 109,458,022 1.71 × 10-1 1.32 × 10 -5 IFT57/HHLA2
FNBMDf rs950649 3 121,567,065 7.63 × 10-4 2.00 × 10 -5 FSTL1
NSA1 rs432446 4 127,906,277 2.84 × 10-2 5.19 × 10 -6  
FNBMD rs922028 4 181,162,903 9.55 × 10-3 1.53 × 10 -5  
FNBMD rs1823926 5 119,882,620 2.62 × 10-1 1.27 × 10 -5 PRR16
NSA1 rs10503733 8 23,589,963 4.29 × 10-4 1.79 × 10 -5 NKX3-1
NSAm rs10503953 8 33,917,325 1.86 × 10-3 1.32 × 10 -5  
NSAf rs4876377 8 118,556,170 4.56 × 10-2 1.93 × 10 -5 THRAP6
NSAf rs10505600 8 133,882,045 2.48 × 10-1 1.36 × 10 -5 PHF20L1
NSA1 rs1552896 9 14,831,387 4.02 × 10-1 8.87 × 10 -6 FREM1
NeckZ1rm rs7857590 9 18,979,893 1.36 × 10-1 8.08 × 10 -6 C9orf138
BUA rs700760 9 86,164,178 3.82 × 10-2 1.42 × 10 -5 ZCCHC6
FNBMDf rs2378731 9 87,175,111 5.53 × 10-4 1.21 × 10 -5  
LSBMDm rs10512315 9 103,334,877 1.70 × 10-1 2.28 × 10 -5  
NeckW1rf rs2048741 9 117,716,816 5.49 × 10-3 2.40 × 10 -5  
ShaftZ1rm rs6744 9 124,988,623 9.58 × 10-2 1.05 × 10 -5 C9orf126
NeckLengf rs773985 10 34,822,758 3.18 × 10-2 1.05 × 10 -5 PARD3
NeckLengf rs10490924 10 124,204,438 1.11 × 10-1 1.80 × 10 -5 PLEKHA1/HTRA1
FNBMDm rs10508076 13 101,270,253 5.41 × 10-3 4.35 × 10 -6 FGF14
TRBMD rs1865968 16 57,535,751 1.15 × 10-1 1.72 × 10 -5  
TRBMD rs1209921 21 39,078,145 2.51 × 10-4 2.41 × 10 -5 C21orf24/ETS2
FNBMDf Same as above    5.32 × 10-5 6.65 × 10 -3  
2c. Magnitude and Location of Peak LOD scores >2.5 for regions in the bone density and geometry phenotype group
Phenotype marker Chrom. physical location maxLOD 1.5 LOD confidence interval  
NeckLeng1 rs1759687 1 112,663,861 2.80 102,547,964–119,889,867  
ShaftW1 rs2320625 2 95,284,610 2.85 85,198,107–105,339,005  
NSA1 rs1304771 2 123,061,290 2.80 108,949,962–129,987,436  
BUA rs842288 3 16,291,319 2.08 8,499,321–40,075,261  
NeckZ1 rs1386389 4 112,310,874 2.33 102,722,423–131,391,829  
NeckW1 rs2094541 10 130,314,425 2.56 128,465,158–135,165,518  
LSBMD rs10492028 12 111,799,883 2.10 103,438,302–117,318,152  
ShaftZ1 rs10518923 15 55,573,538 3.02 51,336,679–58,934,236  
NeckW1 AFM049xd2 16 22,945,152 2.34 16,856,153–24,665,428  
BUA rs10492922 16 27,519,162 2.20 26,434,120–50,596,704  
NeckZ1 rs6502901 17 5,864,832 2.37 451,209–8,829,083  
BUA rs8081154 17 46,196,038 2.12 37,926,265–62,642,504  
NeckW1 rs750160 20 649,631 2.10 161,523–4,335,440  
ShaftZ1 rs7290139 22 44,039,280 3.01 35,890,398–48,603,847  
  1. * SNP in a gene(s) or near (within 60 kb)