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 | Â |
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 |  |