|
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
|
- 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)
