International Journal of Genomics

Research Article

Meta-Analysis of Genome-Wide Association Studies Identifies Novel Functional CpG-SNPs Associated with Bone Mineral Density at Lumbar Spine

Table 1

Significant/suggestive CpG-SNPs for lumbar spine BMD.


CpG-SNP	Chr	Position	Alleles	Nearest gene	Feature	Meta value	GEFOS value	Joint value

rs2941741	6	152008982	G/A	ESR1	Intronic	6.50E − 06	1.21E − 08	2.45E − 12
rs3020333	6	152010254	A/G	ESR1	Intronic, 5 upstream	7.17E − 06	1.57E − 09	3.73E − 13
rs7455028	6	152034386	C/T	ESR1	Intronic	4.57E − 05	0.00013	1.18E − 07
rs13254554	8	120010805	T/C	COLEC10/TNFRSF11B	Intronic	8.99E − 07	1.10E − 19	5.79E − 24
rs2220189	8	120007708	C/G	COLEC10/TNFRSF11B	Intronic	1.53E − 06	4.25E − 20	3.84E − 24
rs525592	11	68195104	C/T	LRP5	Intronic	1.86E − 07	8.69E − 11	6.41E − 16
rs689179	11	68179166	A/G	LRP5	Intronic	2.68E − 07	NA	NA
rs576118	11	68177708	G/A	LRP5	Intronic	2.70E − 07	3.81E − 06	2.95E − 11
rs471966	11	68173861	C/T	LRP5	Intronic	3.29E − 07	NA	NA
rs1784235	11	68185500	C/T	LRP5	Intronic	3.92E − 07	2.95E − 08	3.82E − 13
rs640569	11	68184820	A/G	LRP5	Intronic	4.04E − 07	2.17E − 08	2.92E − 13
rs667126	11	68177728	C/T	LRP5	Intronic	7.80E − 07	NA	NA
rs497261	11	68192244	T/C	LRP5	Intronic	7.83E − 07	1.86E − 11	5.79E − 16
rs314751	11	68179560	C/T	LRP5	Intronic	1.31E − 06	1.20E − 11	6.24E − 16
rs23691	11	68178668	G/A	LRP5	Intronic	1.33E − 06	1.17E − 11	6.18E − 16
rs531163	11	68194496	A/G	LRP5	Intronic	1.35E − 06	9.05E − 11	4.60E − 15
rs9535889	13	52733634	C/G	NEK3	Intronic, 5 upstream, 5 UTR	7.55E − 07	0.469098	5.61E − 06
rs3783242	13	52717950	C/T	NEK3	Intronic, 3 downstream	2.41E − 06	NA	NA
rs9526841	13	52726476	A/G	NEK3	Intronic, 3 downstream	6.64E − 06	0.325285	3.03E − 05
rs2897976	13	52715944	G/A	NEK3	Intronic	9.71E − 06	0.471396	6.08E − 05
rs9526843	13	52730056	C/T	NEK3	Intronic	1.17E − 05	NA	NA
rs2408609	13	52714043	C/T	NEK3	Intronic	1.32E − 05	0.546887	9.26E − 05
rs2408611	13	52709742	G/A	NEK3	Intronic, 5 upstream	2.50E − 05	NA	NA
rs7231498	18	77189387	A/G	NFATC1	Intronic	4.22E − 05	0.000944	7.18E − 07

Note: CpG-SNPs reached a genome-wide significance level ( value ≤ 7.86 × 10⁻⁷) in discovery meta-analysis and/or joint analysis of discovery, and replication studies are marked in bold. Gene/CpG-SNP reported in previous GWAS for BMD is marked in italics. NA: SNPs were not available in the GEFOS 2015 data release. This result was based on the GEFOS 2012 data release because this SNP is not available in the 2015 release.