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

Table 2

Functional annotation of significant/suggestive CpG-SNPs.

CpG-SNPs	Nearest gene	Chromatin state in PBMs^1	Tissues/cells with enhancer histone marks (H3K4me1/H3K27ac)	Motifs changed	eQTL hits
rs2941741	ESR1	Quiescent/low
rs3020333	ESR1	Quiescent/low	Liver	Pou2f2
rs7455028	ESR1	Quiescent/low		5 altered motifs
rs13254554	COLEC10/TNFRSF11B	Quiescent/low		TCF12, p53	3 hits
rs2220189	COLEC10/TNFRSF11B	Quiescent/low	7 tissues		2 hits
rs525592	LRP5	Quiescent/low		4 altered motifs	2 hits
rs689179	LRP5	Quiescent/low	6 tissues	5 altered motifs	1 hit
rs576118	LRP5	Quiescent/low	IPSC, muscle, heart	TAL1	1 hit
rs471966	LRP5	Quiescent/low	8 tissues	8 altered motifs	2 hits
rs1784235	LRP5	Quiescent/low	Blood	AP-2, ELF1, Rad21	1 hit
rs640569	LRP5	Quiescent/low	Blood	Irf, Pax-4, Pou2f2	1 hit
rs667126	LRP5	Quiescent/low	IPSC, muscle, heart	9 altered motifs	2 hits
rs497261	LRP5	Quiescent/low	Muscle	Pax-5, Smad	5 hits
rs314751	LRP5	Quiescent/low	6 tissues	4 altered motifs	4 hits
rs23691	LRP5	Quiescent/low	6 tissues	5 altered motifs	4 hits
rs531163	LRP5	Quiescent/low		7 altered motifs	3 hits
rs9535889	NEK3	Active TSS	24 tissues^2	Rad21, SP1, TATA	72 hits
rs3783242	NEK3	Quiescent/low		CDP, Pou2f2	72 hits
rs9526841	NEK3	Strong transcription		HIF1, RFX5, TCF11::MafG	62 hits
rs2897976	NEK3	Quiescent/low			79 hits
rs9526843	NEK3	Quiescent/low	Intestine		73 hits
rs2408609	NEK3	Quiescent/low		6 altered motifs	78 hits
rs2408611	NEK3	Strong transcription		4 altered motifs	80 hits
rs7231498	NFATC1	Weak transcription	Blood	7 altered motifs

Note: ¹Chromatin state information was retrieved using a 15-state model from the Roadmap Epigenomics Project based on the 5 core histone marks. ²Tissues/cells with promoter histone marks (H3K4me3/H3K9ac). Abbreviation: IPSC: induced pluripotent stem cells.