Table 2.
UKB Results from Stage 1 and Stage 2 (Internal Replication) for the 20 Signals for FEV1/FVC*
| Gene | SNP | Chr | BP | EA | EAF | Functional Consequence† | Blood eQTL P Value | Lung eQTL P Value | Stage 1
(n = 207,616) |
Stage 2 (Internal Replication)
(n = 138,411) |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| β‡ | SE | P Value | β‡ | SE | P Value | |||||||||
| CSNK2B | rs3117579 | 6 | 31,633,496 | G | 0.80 | 5′ UTR variant | 1.1 × 10−4 | 0.025 | 0.24 | 0.02 | 1.2 × 10−23 | 0.19 | 0.03 | 2.0 × 10−11 |
| CTNND1 | rs665058 | 11 | 57,579,166 | T | 0.56 | Intron variant | 5.5 × 10−12 | 0.460 | −0.08 | 0.02 | 1.0 × 10−5 | −0.12 | 0.02 | 1.6 × 10−7 |
| ELN | rs2528794 | 7 | 73,480,805 | G | 0.88 | Intron variant | NA | 0.413 | −0.13 | 0.03 | 7.5 × 10−6 | −0.13 | 0.04 | 1.7 × 10−4 |
| FARP2 | rs377324224 | 2 | 242,393,182 | TG | 0.63 | Intron variant | NA | NA | 0.08 | 0.02 | 9.5 × 10−5 | 0.09 | 0.02 | 1.1 × 10−4 |
| FGFR3 | rs3135877 | 4 | 1,804,276 | G | 0.96 | Intron variant | NA | 0.479 | −0.24 | 0.05 | 9.4 × 10−7 | −0.34 | 0.06 | 7.0 × 10−9 |
| FGFR4 | rs3135911 | 5 | 176,513,896 | C | 0.71 | 5′ UTR variant | 9.5 × 10−6 | 0.359 | 0.10 | 0.02 | 8.0 × 10−7 | 0.10 | 0.03 | 7.5 × 10−5 |
| GFI1 | rs150037086 | 1 | 92,952,080 | G | 0.31 | Intron variant | 1.6 × 10−18§ | NA | 0.11 | 0.02 | 1.8 × 10−7 | 0.11 | 0.03 | 8.0 × 10−6 |
| GJE1 | rs225607 | 6 | 142,455,130 | C | 0.54 | Missense variant | NA | NA | 0.10 | 0.02 | 1.1 × 10−7 | 0.13 | 0.02 | 2.1 × 10−8 |
| KAT7 | rs755736 | 17 | 47,891,904 | A | 0.34 | Intron variant | 3.5 × 10−4 | 0.439 | 0.07 | 0.02 | 5.4 × 10−4 | 0.09 | 0.02 | 1.1 × 10−4 |
| MAPRE1 | rs853854 | 20 | 31,420,757 | T | 0.48 | Intron variant | 3.0 × 10−34 | NA | −0.08 | 0.02 | 3.2 × 10−5 | −0.08 | 0.02 | 2.1 × 10−4 |
| NFATC3 | rs548092276 | 16 | 68,210,935 | C | 0.84 | Intron variant | NA | NA | −0.16 | 0.03 | 3.6 × 10−9 | −0.16 | 0.03 | 7.5 × 10−7 |
| PDGFB | rs2267406 | 22 | 39,633,749 | T | 0.25 | Intron variant | 9.8 × 10−184 | 0.396 | −0.09 | 0.02 | 2.1 × 10−5 | −0.12 | 0.03 | 1.1 × 10−5 |
| PPARD | rs2267666 | 6 | 35,370,728 | A | 0.24 | Intron variant | 0.002 | 5.9 × 10−4 | −0.13 | 0.02 | 5.2 × 10−9 | −0.10 | 0.03 | 7.0 × 10−5 |
| RARA | rs2715554 | 17 | 38,489,170 | A | 0.85 | Intron variant | 3.6 × 10−4 | 0.568 | 0.16 | 0.03 | 2.2 × 10−9 | 0.12 | 0.03 | 1.5 × 10−4 |
| RUNX3 | rs9438876 | 1 | 25,241,116 | A | 0.49 | Intron variant | 8.9 × 10−17 | 0.323 | 0.11 | 0.02 | 4.1 × 10−9 | 0.10 | 0.02 | 2.4 × 10−5 |
| SERPING1 | rs11229063 | 11 | 57,369,730 | G | 0.73 | Intron variant | 7.2 × 10−253 | 0.079 | 0.12 | 0.02 | 2.3 × 10−8 | 0.12 | 0.03 | 2.5 × 10−6 |
| SFRP2 | rs17030437 | 4 | 154,704,225 | C | 0.75 | Intron variant | 7.2 × 10−80 | 0.776 | 0.10 | 0.02 | 1.1 × 10−5 | 0.10 | 0.03 | 1.5 × 10−4 |
| SOX9 | rs796209434 | 17 | 70,122,505 | CT | 0.53 | 3′ UTR variant | NA | NA | −0.04 | 0.02 | 2.4 × 10−2 | −0.08 | 0.02 | 4.3 × 10−4 |
| TCF7L1 | rs4346385 | 2 | 85,504,989 | A | 0.29 | Intron variant | 0.002 | 0.006 | −0.08 | 0.02 | 1.6 × 10−4 | −0.09 | 0.03 | 3.1 × 10−4 |
| WNT7A | rs73151668 | 3 | 13,920,594 | G | 0.85 | Intron variant | 0.281 | 1.1 × 10−5 | −0.11 | 0.03 | 3.0 × 10−5 | −0.21 | 0.03 | 9.5 × 10−11 |
For definition of abbreviations, see Table 1.
*
FEV1/FVC expressed as a percentage.
†
Functional consequence for SNPs with different consequences associated with different transcripts; we considered the most deleterious.
‡
Per-allele effect estimate.
§
Expression data for proxy rs4565725 (r2 = 0.84).