When we queried the FHS 100K association results, several SNPs in previously well-studied candidate genes for osteoporosis were identified (FBAT or GEE p < 0.05), such as rs1801133 in MTHFR; rs1884052 and rs3778099 in ESR1; rs4988300 in LRP5; rs2189480 in VDR; rs2075555 in COLIA1; rs10519297 and rs2008691 in CYP19. We also examined SNPs in other candidate genes of interest to our group such as SNPs in PPARG (rs10510418 and rs2938392) that were associated with BMD and ultrasound and SNPs in ANKH (rs2454873 and rs379016) that were associated with femoral neck section modulus. Here, MTHFR is linked to osteoporosis.