Table 1.
UKB Results from Stage 1 and Stage 2 (Internal Replication) for the 17 Signals for 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 | |||||||||
| ACTN3 | rs57127845 | 11 | 66,318,325 | C | 0.82 | Intron variant | 7.4 × 10−6 | 0.022 | −12.3 | 2.4 | 2.5 × 10−7 | −14.7 | 2.9 | 2.3 × 10−7 |
| ACTN4 | rs189809900 | 19 | 39,147,164 | A | 0.98 | Intron variant | 0.112 | 0.005 | −25.7 | 7.2 | 3.5 × 10−4 | −35.8 | 8.9 | 2.8 × 10−5 |
| CLDN20 | rs34268254 | 6 | 155,590,120 | TA | 0.39 | Intron variant | NA | NA | 10.2 | 1.9 | 4.5 × 10−8 | 9.0 | 2.3 | 4.6 × 10−5 |
| GSK3B | rs6805251 | 3 | 119,560,606 | T | 0.38 | Intron variant | 3.0 × 10−97 | 1.1 × 10−5 | 7.4 | 1.9 | 6.8 × 10−5 | 8.0 | 2.3 | 2.1 × 10−4 |
| HOXA1 | rs45571645 | 7 | 27,135,096 | G | 0.98 | Missense variant | 2.7 × 10−5 | 0.324 | 33.3 | 6.8 | 9.8 × 10−7 | 28.7 | 8.3 | 2.9 × 10−4 |
| HOXB4 | rs201603635 | 17 | 46,653,038 | T | 0.94 | 3′ UTR variant | NA | NA | −12.8 | 3.8 | 6.9 × 10−4 | −16.3 | 4.6 | 1.9 × 10−4 |
| KAT8 | rs138259061 | 16 | 31,136,066 | A | 0.64 | Intron variant | 3.5 × 10−70§ | 2.8 × 10−23§ | −8.7 | 1.9 | 4.1 × 10−6 | −7.7 | 2.3 | 4.5 × 10−4 |
| ITGB5 | rs17282078 | 3 | 124,481,760 | T | 0.87 | 3′ UTR variant | 3.2 × 10−6 | 0.326 | 9.1 | 2.7 | 7.4 × 10−4 | 15.7 | 3.3 | 9.0 × 10−7 |
| MMP24 | rs7280 | 20 | 33,864,484 | A | 0.58 | 3′ UTR variant | 2.2 × 10−36 | 0.499 | 10.3 | 1.8 | 2.7 × 10−8 | 9.7 | 2.3 | 9.5 × 10−6 |
| NCOR2 | rs72451021 | 12 | 124,811,393 | ACT | 0.89 | Intron variant | 6.3 × 10−11‖ | 0.429 | 12.8 | 2.9 | 1.2 × 10−5 | 12.8 | 3.6 | 1.9 × 10−4 |
| NR3C1 | rs72801051 | 5 | 142,685,670 | A | 0.84 | Intron variant | 1.1 × 10−8 | 0.352 | 12.1 | 2.4 | 6.9 × 10−7 | 10.7 | 3.0 | 1.6 × 10−4 |
| ROR2 | rs12684752 | 9 | 94,682,990 | T | 0.94 | Intron variant | 1.4 × 10−9 | 0.266 | −13.8 | 3.9 | 3.7 × 10−4 | −17.8 | 4.7 | 8.5 × 10−5 |
| RUNX1 | rs12483501 | 21 | 36,224,276 | T | 0.63 | Intron variant | 0.926 | NA | 8.9 | 2.0 | 9.3 × 10−6 | 10.1 | 2.5 | 2.1 × 10−5 |
| SERPINC1 | rs2227603 | 1 | 173,882,548 | A | 0.97 | Intron variant | 0.967 | 0.776 | −21.6 | 5.4 | 5.8 × 10−5 | −23.1 | 6.6 | 2.5 × 10−4 |
| SOX9 | rs796209434 | 17 | 70,122,505 | CT | 0.53 | 3′ UTR variant | NA | NA | 7.3 | 1.8 | 6.2 × 10−5 | 7.9 | 2.2 | 2.0 × 10−4 |
| WNT2B | rs351370 | 1 | 113,054,659 | C | 0.41 | Intron variant | 0.191 | 6.9 × 10−4 | 7.0 | 1.8 | 1.2 × 10−4 | 7.7 | 2.2 | 3.2 × 10−4 |
| WNT9A | rs35799012 | 1 | 228,133,322 | C | 0.83 | Intron variant | 0.322 | 0.041 | −7.9 | 2.4 | 9.1 × 10−4 | −13.5 | 2.9 | 2.2 × 10−6 |
Definition of abbreviations: BP = base position (build GRCh37); Chr = chromosome; EA = effect allele; EAF = EA frequency; eQTL = expression quantitative trait loci; NA = not available; UKB = UK Biobank; UTR = untranslated region.
*
FVC in milliliters.
†
Functional consequence for SNPs with different consequences associated with different transcripts; we considered the most deleterious.
‡
Per-allele effect estimate.
§
Expression data for proxy rs9936329 (r2 = 0.95).
‖
Expression data for proxy rs11057583 (r2 = 1.0).