A genome-wide association study identifies risk loci for spirometric measures among smokers of European and African ancestry

Lutz, Sharon M.; Cho, Michael H.; Young, Kendra; Hersh, Craig P.; Castaldi, Peter J.; McDonald, Merry-Lynn; Regan, Elizabeth; Mattheisen, Manuel; DeMeo, Dawn L.; Parker, Margaret; Foreman, Marilyn; Make, Barry J.; Jensen, Robert L.; Casaburi, Richard; Lomas, David A.; Bhatt, Surya P.; Bakke, Per; Gulsvik, Amund; Crapo, James D.; Beaty, Terri H.; Laird, Nan M.; Lange, Christoph; Hokanson, John E.; Silverman, Edwin K.

doi:10.1186/s12863-015-0299-4

Table 4 Comparison of the current GWA results with the novel genome wide results from the largest GWAS of pre bronchodilator FEV₁ and FEV₁/FVC ratio in the CHARGE/SpiroMeta consortium

From: A genome-wide association study identifies risk loci for spirometric measures among smokers of European and African ancestry

chr	Gene	SNP/Position (bp)	Phenotype	CHARGE/SpiroMeta	COPDGene NHW	COPDGene AA	Meta-analysis: COPDGene, ECLIPSE, and GenKOLS
chr	Gene	SNP/Position (bp)	Phenotype	Coded Allele/Beta/P-value	Coded Allele/Allele Frequency/Beta/P-value
1	MFAP2	rs2284746	FEV₁/FVC	G/-0.04/7.50e-16	G/0.476/0.007/0.012	G/0.807/0.005/0.256	C/0.545/0.007/1.4E-04
1	MFAP2	17306675	FEV₁/FVC	G/-0.04/7.50e-16	G/0.476/0.007/0.012	G/0.807/0.005/0.256	C/0.545/0.007/1.4E-04
1	TGFB2	rs993925*	FEV₁/FVC	T/0.034/1.16e-08	C/0.33/0.002/0.551	C/0.32/0.004/0.232	T/0..594/0.002/0.3655
1	TGFB2	218860068	FEV₁/FVC	T/0.034/1.16e-08	C/0.33/0.002/0.551	C/0.32/0.004/0.232	T/0..594/0.002/0.3655
2	TNS1	rs2571445	FEV₁	G/0.047/9.83e-11	G/0.393/-0.027/0.03526	G/0/201/0.007/0.7201	A/0.645/-0.015/0.0996
2	TNS1	218683154	FEV₁	G/0.047/9.83e-11	G/0.393/-0.027/0.03526	G/0/201/0.007/0.7201	A/0.645/-0.015/0.0996
2	HDAC4	rs12477314	FEV₁/FVC	T/0.041/1.68e-08	T/0.8/-0.001/0.8196	T/0.963/-0.003/0.683	T/0.187/0.003/0.1802
2	HDAC4	239877148	FEV₁/FVC	T/0.041/1.68e-08	T/0.8/-0.001/0.8196	T/0.963/-0.003/0.683	T/0.187/0.003/0.1802
3	RARB	rs1529672	FEV₁/FVC	C/-0.048/3.97e-14	C/0.162/0.015/1.88E-05	C/0.20/0.005/0.2018	A/0.82/0.01/6.72E-06
3	RARB	25520582	FEV₁/FVC	C/-0.048/3.97e-14	C/0.162/0.015/1.88E-05	C/0.20/0.005/0.2018	A/0.82/0.01/6.72E-06
3	MECOM	rs1344555	FEV₁	T/-0.034/2.65e-08	T/0.809/0.017/0.293	T/0.799/-0.037/0.07322	T/0.194/-0.008/0.4903
3	MECOM	169300219	FEV₁	T/-0.034/2.65e-08	T/0.809/0.017/0.293	T/0.799/-0.037/0.07322	T/0.194/-0.008/0.4903
4	FAM13A	rs2045517	FEV₁/FVC	T/-0.047/2.0e-11	T/0.595/0.012/5.32E-06	T/0.343/0.005/0.1522	T/0.485/-0.012/5.66E-12
4	FAM13A	89870964	FEV₁/FVC	T/-0.047/2.0e-11	T/0.595/0.012/5.32E-06	T/0.343/0.005/0.1522	T/0.485/-0.012/5.66E-12
4	GSTCD	rs10516526	FEV₁	G/0.108/4.75e-14	G/0.935/-0.117/6.16E-06	G/0.951/0.002/0.9647	A/0.694/-0.066/0.00029
4	GSTCD	106688904	FEV₁	G/0.108/4.75e-14	G/0.935/-0.117/6.16E-06	G/0.951/0.002/0.9647	A/0.694/-0.066/0.00029
4	NPNT	rs17331332	FEV₁	G/-0.102/1.11e-12	A/0.933/-0.128/6.16E-06	A/0.979/-0.14/0.03813	A/0.064/0.093/3.19E-06
4	NPNT	106808107	FEV₁	G/-0.102/1.11e-12	A/0.933/-0.128/6.16E-06	A/0.979/-0.14/0.03813	A/0.064/0.093/3.19E-06
4	HHIP	rs1032296	FEV₁/FVC	T/-0.05/3.42e-12	C/0.413/-0.011/1.82E-05	C/0.17/-0.01/0.023	T/0.59/-0.011/1.80E-08
4	HHIP	145434688	FEV₁	T/-0.047/8.74e-11	A/0.414/-0.045/0.0004	A/0.17/-0.061/0.004	T/0.585/-0.048/2.27E-07
5	SPATA9	rs153916	FEV₁/FVC	T/-0.031/2.12e-08	C/0.539/-0.008/0.002	C/0.57/-0.008/0.017	T/0.55/-0.008/3.06E-05
5	SPATA9	95036700	FEV₁/FVC	T/-0.031/2.12e-08	C/0.539/-0.008/0.002	C/0.57/-0.008/0.017	T/0.55/-0.008/3.06E-05
5	HTR4	rs11168048	FEV₁/FVC	T/-0.047/5.97e-11	T/0.42/0.01/0.0102	T/0.23/-0.002/0.5213	T/0.425/-0.004/0.04823
5	HTR4	145479139	FEV₁	T/-0.046/2.43e-10	T/0.42/0.03/0.008	T/0.23/0.01/0.548	T/0.428/-0.02/0.01452
5	ADAM19	rs11134779	FEV₁/FVC	G/-0.042/6.01e-09	G/0.65/0.005/0.086	G/0.411/0.007/0.024	A/0.574/0.006/8.00E-04
5	ADAM19	156936766	FEV₁/FVC	G/-0.042/6.01e-09	G/0.65/0.005/0.086	G/0.411/0.007/0.024	A/0.574/0.006/8.00E-04
6	AGER	rs2070600	FEV₁/FVC	T/0.126/9.07e-15	A/0.043/0.035/6.22E-08	A/0.01/-0.003/0.849	T/0.31/0.026/2.24e-07
6	AGER	32151443	FEV₁	T/0.025/1.271e-12	C/0.043/0.121/0.0001	A/0.01/0.054/0.522	T/0.302/0.081/7.43e-04
6	GPR126	rs3817928	FEV₁/FVC	G/0.059/2.27e-12	G/0.806/-0.003/0.311	G/0.802/-0.015/3e-04	A/0.807/-0.006/0.01394
6	GPR126	142750516	FEV₁/FVC	G/0.059/2.27e-12	G/0.806/-0.003/0.311	G/0.802/-0.015/3e-04	A/0.807/-0.006/0.01394
6	LOC153910	rs262129	FEV₁/FVC	G/0.056/2.91e-13	G/0.704/-0.006/0.043	G/0.19/-0.004/0.3078	A/0.59/-0.005/0.009
6	LOC153910	142853144	FEV₁/FVC	G/0.056/2.91e-13	G/0.704/-0.006/0.043	G/0.19/-0.004/0.3078	A/0.59/-0.005/0.009
6	ZKSCAN3	rs6903823	FEV₁	G/-0.037/2.18e-10	G/0.777/0.013/0.380	G/0.592/-0.049/0.00233	A/0.712/-0.013/0.193
6	ZKSCAN3	28322296	FEV₁	G/-0.037/2.18e-10	G/0.777/0.013/0.380	G/0.592/-0.049/0.00233	A/0.712/-0.013/0.193
6	NCR3	rs2857595	FEV₁/FVC	G/0.037/2.28e-10	G/0.188/0/0.9309	G/0.423/-0.001/0.7777	A/0/-0.001/0.6174
6	NCR3	31568469	FEV₁/FVC	G/0.037/2.28e-10	G/0.188/0/0.9309	G/0.423/-0.001/0.7777	A/0/-0.001/0.6174
6	ARMC2	rs2798641	FEV₁/FVC	T/-0.041/8.35e-09	C/0.191/-0.009/0.005	C/0.053/-0.005/0.505	T/0.825/-0.008
		109268050					T/0.825/-0.008
		109268050					0.002
9	PTCH1	rs16909859	FEV₁/FVC	G/0.08/7.45e-10	G/0.075/-0.004/0.432	G/0.295/-0.005/0.156	A/0.67/-0.004/0.1468
9	PTCH1	98204792	FEV₁/FVC	G/0.08/7.45e-10	G/0.075/-0.004/0.432	G/0.295/-0.005/0.156	A/0.67/-0.004/0.1468
10	CDC123	rs7068966	FEV₁/FVC	T/0.033/6.13e-13	C0.522/0.002/0.516	T/0.782/-0.008/0.04255	T/0.449/0.003/0.07659
10	CDC123	12277992	FEV₁/FVC	T/0.033/6.13e-13	C0.522/0.002/0.516	T/0.782/-0.008/0.04255	T/0.449/0.003/0.07659
10	C10orf1	rs11001819	FEV₁	G/-0.029/2.98e-12	A/0.524/-0.009/0.493	A/0.661/0.012/0.4849	A/0.45/0.006/0.472
10	C10orf1	78315224	FEV₁	G/-0.029/2.98e-12	A/0.524/-0.009/0.493	A/0.661/0.012/0.4849	A/0.45/0.006/0.472
12	LRP1	rs11172113	FEV₁/FVC	T/-0.032/1.24e-08	T/0.407/0.006/0.038	T/0.428/0.004/0.1701	T/0.415/-0.004/0.01385
12	LRP1	57527283	FEV₁/FVC	T/-0.032/1.24e-08	T/0.407/0.006/0.038	T/0.428/0.004/0.1701	T/0.415/-0.004/0.01385
12	CCDC38	rs1036429	FEV₁/FVC	T/0.038/2.30e-11	C/0.21/0.006/0.050	C/0.162/0.004/0.399	T/0.809/0.004/0.06425
12	CCDC38	96271428	FEV₁/FVC	T/0.038/2.30e-11	C/0.21/0.006/0.050	C/0.162/0.004/0.399	T/0.809/0.004/0.06425
15	THSD4	rs12899618	FEV₁/FVC	G/0.076/1.86e-15	G/0.152/-0.012/0.0007	G/0.12/-0.009/0.0507	A/0.854/-0.009/2.8e-04
15	THSD4	71645120	FEV₁/FVC	G/0.076/1.86e-15	G/0.152/-0.012/0.0007	G/0.12/-0.009/0.0507	A/0.854/-0.009/2.8e-04
16	MMP15	rs12447804	FEV₁/FVC	T/-0.038/3.59e-08	T/0.79/-0.002/0.598	T/0.938/-0.001/0.911	T/0.191/0.002/0.528
16	MMP15	58075282	FEV₁/FVC	T/-0.038/3.59e-08	T/0.79/-0.002/0.598	T/0.938/-0.001/0.911	T/0.191/0.002/0.528
16	CFDP1	rs2865531	FEV₁/FVC	T/0.031/1.77e-11	T/0.592/-0.005/0.078	T/0.351/-0.006/0.05393	A/0.522/-0.005/0.0742
16	CFDP1	75390316	FEV₁/FVC	T/0.031/1.77e-11	T/0.592/-0.005/0.078	T/0.351/-0.006/0.05393	A/0.522/-0.005/0.0742
21	KCNE2	rs9978142	FEV₁/FVC	T/-0.043/2.65e-08	T/0.849/0.002/0.558	T/0.799/0.002/0.530	A/0.83/0.001/0.677
21	KCNE2	35652239	FEV₁/FVC	T/-0.043/2.65e-08	T/0.849/0.002/0.558	T/0.799/0.002/0.530	A/0.83/0.001/0.677

The SNP with the lowest p value within each region or gene from the CHARGE/Spirometa consortium is listed ordered by chromosome number [10]. Quite a few SNPs met a nominal levels of significance using Bonferroni correction (P < 0.0018 for the 28 regions tested)
*In Table 4, while this SNP is not significant in our cohort and meta-analysis, rs12048582 in the TGFB2 gene was genome wide significant (p-value = 6.28E-09)

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