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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

VariantLocationEAOAEAFβGWASGeneExpressionaDistance to TSSPeQTLβeQTL
rs4683184chr3:46146215GA0.37− 0.01CCR522.96 ± 7.33− 224,6382.06E−04− 0.47
rs13072536chr3:52827195TA0.220.02SFMBT12.87 ± 0.59− 219,5561.43E−040.50
rs1991431chr3:141414608AG0.44− 0.02ZBTB387.13 ± 1.5790,3957.68E−050.44
rs1550270chr4:165340648CT0.330.02CPE4.64 ± 3.7− 20,5467.29E−060.51
rs798545chr7:2722752TC0.230.01GNA1221.9 ± 4.75− 121,5737.94E−050.53
rs2551769chr7:135453583AG0.280.01CALD11.23 ± 1.05709,3281.38E−05− 0.58
rs11245388chr10:124850559TG0.47− 0.01METTL101.06 ± 0.1958,6881.47E−110.72
rs3212240chr14:24341692CT0.43− 0.01RIPK34.51 ± 1.0716461.47E−06− 0.55
rs7147775chr14:75203508GT0.44− 0.02EIF2B24.62 ± 0.58200,5972.16E−09− 0.62
rs7147775chr14:75203508GT0.44− 0.02ACYP11.8 ± 0.56134,0244.75E−060.55
rs11073930chr15:90503480GC0.46− 0.02IQGAP166.34 ± 9.26115,2621.46E−100.66
rs1736213chr17:17231214TG0.430.01FLCN4.06 ± 0.89− 59751.82E−09− 0.54
rs1661725chr17:75564053CT0.440.01LLGL20.7 ± 0.2438,9739.98E−07− 0.55
rs77420750chr19:15868934AC0.310.01TMEM38A0.49 ± 0.29− 792,1941.43E−040.45
rs314675chr19:46692822CT0.1− 0.02FKRP1.45 ± 0.27− 53,2245.88E−060.92
rs73066226chr19:58496846CT0.170.01UBE2M22.85 ± 3.39− 62,1151.71E−060.66
rs5754387chr22:21620414CG0.17− 0.02UBE2L320.1 ± 2.8870,9671.82E−050.46
rs2294358chr22:36375211CG0.070.04FOXRED22.44 ± 1.37− 131,8931.55E−061.11
rs932536chr22:49866824AG0.13− 0.02ZBED45.67 ± 0.6712,9828.39E−060.71
rs5770908chr22:50439289AG0.29− 0.02PPP6R210.17 ± 1.895,9851.36E−040.41
rs5914035chrX:56981783CT0.230.02LINC0142013.14 ± 2.09252,5424.91E−060.62
  1. 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), βGWAS values are relevant to the effect allele and were obtained from Morris et al. [19], βeQTL 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%
  2. aExpression levels are stated as mean reads per kilobase million (RPKM) ± standard deviation