Table 3. Summary of Associations With Gene Expression in Human Bone Biopsies.

Locus	Position (build 36)	SNP	Region	Nearest gene(s) (distance in kb)	Association with the nearest genes		The most significant cis-eQTL
					Beta	p	Gene	Beta	p	FDR p	Distance (kb)
Combined p < 5 × 1 10−8 for trabecular vBMD
1p36.12	22444772	rs12755933	Intergenic	WNT4 (103)	0.030	0.37	EPHB2	−0.062	0.02	0.34	465
1p36.12	22554953	rs 12742784	Intergenic	ZBTB40 (96)	0.105	0.08	EPHB2	0.120	3.49 ×10−5	1.72 × 10−3	355
1q43	238659259	rs9661787	Intronic	FMN2 (0)	0.027	0.27	GREM2	−0.049	0.10	0.61	60
5p13	36516441	rs2468531	Intergenic	SLC1A3 (126)	0.279	4.36 × 10−3	SLC1A3	0.279	4.36 × 10−3	0.01	126
			Intergenic	RANBP3L (179)	−0.107	0.33
8q24	120045437	rs1485303	Intergenic	TNFRSF1 IB (12)	−0.019	0.61	NOV	−0.136	0.04	0.53	452
13q14	41862203	rs17457561	Intergenic Intergenic	AKAP11 (67) TNFSF11 (700)	−0.068 0.035	0.03 0.28	AKAP11	−0.068	0.03	0.32	67
Combined 5 × 10−8 < p < 5 × 10−6 for trabecular vBMD
2p21	54735125	rs2941584	Intronic	SPTBN1	0.039	0.20	EML6	0.096	3.33 × 10−3	0.04	69
6q25	151897286	rs10872673	Intronic Intergenic	C6orf97 (CCDC170) ESR1 (160)	−0.003 0.040	0.92 0.07	MTHFD1L	−0.090	0.03	0.28	433
12p13.3	2378832	rs7301013	Intronic	CACNA1C	0.056	0.17	WNT5B	0.280	1.81 × 10−4	0.01	752
12p12.1	28183168	rs12813778	Intergenic	CCDC91 (118)	n.a.	n.a. 0.41	STK38L	−0.068	0.03	0.15	813
			Intergenic	PTHLH (167)	−0.018
12q21.3	88861177	rs4842697	Intergenic	ATP2B1 (287)	−0.093	0.02	ATP2B1	−0.093	0.02	0.13	287
16p13.3	315783	rs9921222	Intronic	AXIN1	−0.033	0.27	POLR3K	0.102	2.57 × 10−3	0.07	279

Bold values are statistically significant (FDR p < 0.05).

eQTL = expression quantitative trait locus; FDR = false-discovery rate; vBMD = volumetric BMD; n.a. = filtered out because of low signal values in the microarray.