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Table 4 Associations of bone traits with selected candidate genes for osteoporosis with a FBAT or GEE p-value < 0.05

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

Chrom Candidate Gene Published SNP Ref. 100K SNP r2* Physical Position Lowest P-value by GEE GEE Phenotype Lowest P-value by FBAT FBAT Phenotype
1 MTHFR rs1801133 [38] rs1801133 self 11,790,644 0.033 ShaftZ1rm 0.042 NSA1
    [39]        
    [28]        
6 ESR1 rs2234693 [45] rs3866461 0.223 152,238,835 0.014 NSAm 0.003 NeckLengf
     rs1884052 0.004 152,383,480 0.002 ShaftZ1R 0.023 NeckW1rf
     rs3778099 0.002 152,510,689 0.003 BUA 0.019 FNBMD
   rs9340799 [45]        
11 LRP5 rs4988321 [40, 46] rs4988300 no data 67,845,407 0.038 ShaftZ1rm 0.025 FNBMDf
   rs627174   rs4988300 no data      
   rs3736228 [40, 41] rs4988300 0.030      
12 VDR rs11568820 [29] rs2189480 0.049 46,550,095 0.011 NeckZ1rm 0.021 LSBMD
   rs10735810 [29] rs2189480 no data      
   rs1544410 [29] rs2189480 0.045      
   rs7975232 [29] rs2189480 no data      
   rs731236 [29] rs2189480 no data      
15 CYP19 rs700518 [47] rs10519297 0.902 49,328,952 0.002 NSA1 0.859 NSA1
    [48] rs2008691 0.239 49,335,602 0.003 NSA1 0.012 NSA1
   rs4775936 [49] rs10519297 0.58      
   rs10046   rs10519297 0.82      
   rs11575899   rs10519297 no data      
17 COL1A1 rs1107946 [50] rs2075555 no data 45,629,290 0.034 NeckW1rf 0.010 ShaftWm
   rs11327935 [51] rs2075555 no data      
   rs1800012 [52] rs2075555 no data      
  1. * r2 between the 100K SNP and a corresponding published SNP (column to the left)
  2. p-values < 0.005 are shown in bold.