Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts

Mullin, Benjamin H.; Tickner, Jennifer; Zhu, Kun; Kenny, Jacob; Mullin, Shelby; Brown, Suzanne J.; Dudbridge, Frank; Pavlos, Nathan J.; Mocarski, Edward S.; Walsh, John P.; Xu, Jiake; Wilson, Scott G.

doi:10.1186/s13059-020-01997-2

Table 1 Genetic loci demonstrating co-localised eBMD GWAS and osteoclast cis-eQTL associations

From: Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts

Variant	Location	EA	OA	EAF	β_GWAS	Gene	Expression^a	Distance to TSS	P_eQTL	β_eQTL
rs4683184	chr3:46146215	G	A	0.37	− 0.01	CCR5	22.96 ± 7.33	− 224,638	2.06E−04	− 0.47
rs13072536	chr3:52827195	T	A	0.22	0.02	SFMBT1	2.87 ± 0.59	− 219,556	1.43E−04	0.50
rs1991431	chr3:141414608	A	G	0.44	− 0.02	ZBTB38	7.13 ± 1.57	90,395	7.68E−05	0.44
rs1550270	chr4:165340648	C	T	0.33	0.02	CPE	4.64 ± 3.7	− 20,546	7.29E−06	0.51
rs798545	chr7:2722752	T	C	0.23	0.01	GNA12	21.9 ± 4.75	− 121,573	7.94E−05	0.53
rs2551769	chr7:135453583	A	G	0.28	0.01	CALD1	1.23 ± 1.05	709,328	1.38E−05	− 0.58
rs11245388	chr10:124850559	T	G	0.47	− 0.01	METTL10	1.06 ± 0.19	58,688	1.47E−11	0.72
rs3212240	chr14:24341692	C	T	0.43	− 0.01	RIPK3	4.51 ± 1.07	1646	1.47E−06	− 0.55
rs7147775	chr14:75203508	G	T	0.44	− 0.02	EIF2B2	4.62 ± 0.58	200,597	2.16E−09	− 0.62
rs7147775	chr14:75203508	G	T	0.44	− 0.02	ACYP1	1.8 ± 0.56	134,024	4.75E−06	0.55
rs11073930	chr15:90503480	G	C	0.46	− 0.02	IQGAP1	66.34 ± 9.26	115,262	1.46E−10	0.66
rs1736213	chr17:17231214	T	G	0.43	0.01	FLCN	4.06 ± 0.89	− 5975	1.82E−09	− 0.54
rs1661725	chr17:75564053	C	T	0.44	0.01	LLGL2	0.7 ± 0.24	38,973	9.98E−07	− 0.55
rs77420750	chr19:15868934	A	C	0.31	0.01	TMEM38A	0.49 ± 0.29	− 792,194	1.43E−04	0.45
rs314675	chr19:46692822	C	T	0.1	− 0.02	FKRP	1.45 ± 0.27	− 53,224	5.88E−06	0.92
rs73066226	chr19:58496846	C	T	0.17	0.01	UBE2M	22.85 ± 3.39	− 62,115	1.71E−06	0.66
rs5754387	chr22:21620414	C	G	0.17	− 0.02	UBE2L3	20.1 ± 2.88	70,967	1.82E−05	0.46
rs2294358	chr22:36375211	C	G	0.07	0.04	FOXRED2	2.44 ± 1.37	− 131,893	1.55E−06	1.11
rs932536	chr22:49866824	A	G	0.13	− 0.02	ZBED4	5.67 ± 0.67	12,982	8.39E−06	0.71
rs5770908	chr22:50439289	A	G	0.29	− 0.02	PPP6R2	10.17 ± 1.8	95,985	1.36E−04	0.41
rs5914035	chrX:56981783	C	T	0.23	0.02	LINC01420	13.14 ± 2.09	252,542	4.91E−06	0.62

EA effect allele, OA other allele, EAF effect allele frequency (derived from the osteoclast eQTL cohort), eBMD estimated BMD, TSS transcription start site; variant locations derived from dbSNP build 150 (GRCh38/hg38), β_GWAS values are relevant to the effect allele and were obtained from Morris et al. [19], β_eQTL values are given as the normalised effect size on gene expression for the effect allele. eQTL associations are significant using a multiple-testing corrected FDR of 5%
^aExpression levels are stated as mean reads per kilobase million (RPKM) ± standard deviation

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ISSN: 1474-760X

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