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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
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
17306675
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
218860068
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
218683154
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
239877148
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
25520582
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
169300219
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
89870964
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
106688904
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
106808107
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
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
95036700
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
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
156936766
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
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
142750516
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
142853144
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
28322296
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
31568469
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
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
98204792
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
12277992
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
78315224
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
57527283
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
96271428
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
71645120
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
58075282
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
75390316
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
35652239
  1. 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)
  2. *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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BMC Genomic Data

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