Table 2 Associated genetic variants in the discovery sample set (n = 96 cases and n = 96 controls)
From: Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease
Chr | Pos (bp) | SNP rs ID | Alt | Ref | F c (%) | F p (%) | OR (95 % CI) | P value | Gene | Coding | RG score | ExAc Eur frequencya | CADD_PHREDb |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 110230569 | 72989301 | G | A | 10.0 | 22.1 | 2.5 (1.0-6.2) | 0.038 | GSTM1 | 4 | 0.24 | NA | |
1 | 110233057 | 111436983 | C | T | 11.6 | 26.7 | 2.8 (1.2-6.2) | 0.013 | GSTM1 | 7 | 0.24 | NA | |
2 | 216991935 | 12694384 | A | C | 29.4 | 17.9 | 0.5 (0.3-0.9) | 0.04 | XRCC5 | 5 | NA | NA | |
2 | 218669225 | 61741262 | C | T | 13.6 | 0 | NA | 0.027 | TNS1 | p.(Asp1722Ser) | 4 | 0.13 | 12.49 |
2 | 218746990 | 2303381 | T | A | 7.7 | 1.5 | 0.2 (0.0-0.9) | 0.019 | TNS1 | 6 | NA | NA | |
3 | 55520778 | 566926 | T | G | 39.2 | 25.0 | 0.5 (0.3-0.9) | 0.017 | WNT5A | 3a | NA | NA | |
4 | 106638697 | 72671840 | G | A | 2.3 | 11.4 | 5.3 (1.5-18.9) | 5.8 × 10−3 | GSTCD | 6 | NA | NA | |
4 | 106647679 | 72671858 | T | C | 3.0 | 10.5 | 3.7 (1.2-11.7) | 0.026 | GSTCD | 7 | NA | NA | |
4 | 106755996 | 11728716 | A | G | 3.4 | 21.0 | 7.4 (2.5-22.5) | 6.5 × 10−5 | GSTCD | 1f | NA | NA | |
5 | 58284208 | 3805557 | C | T | 22.0 | 11.9 | 0.5 (0.2-0.9) | 0.034 | PDE4D | 7 | NA | NA | |
5 | 58284283 | 3805556 | G | A | 22.0 | 11.8 | 0.5 (0.2-0.9) | 0.033 | PDE4D | 6 | 0.84 | NA | |
5 | 58286625 | 1553114 | C | T | 22.0 | 11.8 | 0.5 (0.2-0.9) | 0.033 | PDE4D | 7 | 0.84 | NA | |
5 | 141993867 | 17223611 | T | C | 10.6 | 3.0 | 0.3 (0.1-0.8) | 0.025 | FGF1 | 5 | NA | NA | |
6 | 142703137 | 2143390 | T | C | 2.9 | 19.2 | 7.9 (1.6-37.6) | 4.5 × 10−3 | GPR126 | p.(Asp373=) | 7 | 0.12 | NA |
6 | 151197501 | 9322290 | C | T | 17.4 | 9.0 | 0.5 (0.2-1.0) | 0.047 | MTHFD1L | 5 | NA | NA | |
6 | 151206894 | 147872265 | T | C | 7.6 | 2.2 | 0.3 (0.1-1.0) | 0.049 | MTHFD1L | 7 | 0.002 | NA | |
6 | 151263456 | 803451 | A | G | 41.8 | 55.7 | 1.8 (1.1-2.9) | 0.04 | MTHFD1L | 7 | NA | NA | |
6 | 151264132 | 803448 | T | C | 37.9 | 50.7 | 1.7 (1.0-2.7) | 0.037 | MTHFD1L | 6 | NA | NA | |
6 | 152183551 | 1643821 | A | G | 25.8 | 39.0 | 1.8 (1.1-3.1) | 0.026 | ESR1 | 6 | NA | NA | |
8 | 42552530 | 41272375 | C | G | 1.5 | 6.9 | 4.8 (1.0-22.8) | 0.034 | CHRNB3 | 5 | NA | NA | |
9 | 98239503 | 3780573 | A | G | 18.3 | 8.7 | 0.4 (0.2-0.9) | 0.041 | PTCH1 | 5 | NA | NA | |
10 | 81706281 | 6413520 | G | A | 0.8 | 5.9 | 8.2 (1.0-66.4) | 0.036 | SFTPD | p.(Ser45=) | 5 | 0.07 | NA |
10 | 123358096 | 41301039 | G | C | 25.0 | 2.8 | 0.1 (0.0-0.7) | 0.017 | FGFR2 | 4 | NA | NA | |
11 | 102738499 | 632009 | T | C | 29.6 | 50.8 | 2.5 (1.5-4.1) | 6.7 × 10−4 | MMP12 | 7 | NA | NA | |
12 | 23737566 | 11046992 | A | G | 21.2 | 33.1 | 1.8 (1.1-3.2) | 0.039 | SOX5 | 6 | NA | NA | |
12 | 110224916 | 60258652 | T | C | 2.4 | 10.5 | 4.7 (1.0-22.9) | 0.05 | TRPV4 | 5 | NA | NA | |
12 | 110224922 | 1861810 | A | C | 36.6 | 53.8 | 2.0 (1.1-3.8) | 0.04 | TRPV4 | 5 | NA | NA | |
12 | 110232032 | 59870578 | A | G | 7.8 | 1.6 | 0.2 (0.0-0.9) | 0.034 | TRPV4 | 4 | NA | NA | |
12 | 110232034 | 59940634 | T | G | 7.8 | 1.6 | 0.2 (0.0-0.9) | 0.034 | TRPV4 | 4 | NA | NA | |
15 | 71434029 | 2004101 | A | T | 0.8 | 5.6 | 7.5 (0.9-61.6) | 0.035 | THSD4 | 7 | NA | NA | |
15 | 78790189 | 2292115 | G | A | 4.8 | 0 | NA | 0.03 | IREB2 | 7 | NA | NA | |
15 | 78911181 | 8040868 | C | T | 31.8 | 47.8 | 2.0 (1.2-3.2) | 8.8 × 10−3 | CHRNA3 | p.(Val53=) | 1f | 0.41 | NA |
16 | 16130514 | 903880 | A | C | 15.9 | 27.2 | 2.0 (1.1-3.6) | 0.027 | ABCC1 | 4 | NA | NA | |
16 | 16205741 | 9673292 | C | G | 4.5 | 0 | NA | 0.013 | ABCC1 | 6 | NA | NA | |
16 | 16230290 | 212087 | A | G | 38.6 | 52.2 | 1.7 (1.1-2.8) | 0.028 | ABCC1 | 5 | 0.44 | NA | |
16 | 16235366 | 113328089 | A | G | 6.9 | 1.5 | 0.2 (0.0-1.0) | 0.034 | ABCC1 | 5 | NA | NA | |
20 | 15967390 | 41275442 | T | C | 9.1 | 17.7 | 2.1 (1.0-4.5) | 0.049 | MACROD2 | p.(Thr100Met) | 4 | 0.18 | 3.98 |