By performing meta-analysis combining the five GWAS datasets, we identified 9 CpG-SNPs that were significantly associated with lumbar spine BMD at a genome-wide significance level ([alpha] = 7.86 x [10.sup.-7]), including 5 novel SNPs rs689179 (p value = 2.68 x [10.sup.-7]), rs576118 (p value = 2.70 x [10.sup.-7]), rs471966 (p value = 3.29 x [10.sup.-7]), rs640569 (p value = 4.04 x [10.sup.-7]), and rs667126 (p value=7.80 x [10.sup.-7]) in LRP5 gene and one SNP rs9535889 in novel gene NEK3 (p value =7.55 x [10.sup.-7]).
Notably, the novel SNPs rs9535889, rs9526841, and rs2408611 in NEK3 gene were all located in regions with strong transcription and enhancer activities in PBMs as well as various other tissues and cell types (Table 2), highlighting strong regulatory potential of these CpG-SNPs.
These BMD-associated CpG-SNPs were mapped to six genes; some of which have not been reported for association with BMD in previous GWAS, such as NEK3 and NFATC1 genes.
In summary, we performed a targeted GWAS analysis for potential functional CpG-SNPs and identified 2 novel BMD-associated genes, NEK3 and NFATC1.
Okano, "Molecular cloning and characterization of the human NIMA-related protein kinase 3 gene (NEK3)," Cytogenetic and Genome Research, vol.