. Author manuscript; available in PMC: 2019 Jun 1.

Published in final edited form as: Mol Genet Genomics. 2018 Jan 11;293(3):711–723. doi: 10.1007/s00438-017-1414-1

Table 3.

The number of SNPs with different criterions

	HDL\|FNK BMD	LDL\|FNK BMD	TC\|FNK BMD	TG\|FNK BMD
cFDR < 0.05 and fdr. GPA < 0.2	160	148	202	122
P > 5E-08	74	68	93	56
Repeat with previous GWAS findings	rs12708980	—	—	—
Had high LD with previous GWAS findings	rs5754467			rs12751742
	(r² = 0.807 with rs181362)	rs2699429	rs2178950	(r² = 0.892 with rs12748152)
	rs9930506	(r² = 0.965 with rs6831256)	(r² = 0.815 with rs2737229)	rs9930506
	(r² = 0.868 with rs1121980)			(r² = 0.868 with rs1121980)

Column definition: HDL | FNK BMD - high density lipoprotein cholesterol conditioned on femoral neck bone mineral density; LDL | FNK BMD - low density lipoprotein cholesterol conditioned on femoral neck bone mineral density; TC | FNK BMD - total cholesterol conditioned on femoral neck bone mineral density; TG | FNK BMD - triglyceride conditioned on femoral neck bone mineral density;

Row definition: cFDR - conditional false discovery rate; fdr. GPA - false discovery rate of GPA when one SNP was associated with PL conditioned on FNK BMD; P - summary statistic p value of original GWAS; LD - linkage disequilibrium; r² - linkage disequilibrium value.