Table 2.
Genes implicated as high-priority genes for novel genome-wide significant and previously-reported signals using expression data and functional annotation. #Variant did not reach P<5.15x10-4 (Bonferroni corrected P value for 97 tests) in this study for any trait. *Gene implicated as it contained a deleterious variant (Supplementary Table 14); all other genes implicated by co-localisation of GWAS and eQTL signal. (*) implicated by both co-localisation of eQTL and GWAS, and a deleterious variant. All 234 genes implicated are listed in Supplementary Table 15.
| Genome-wide significant trait (additional traits with P<5.15x10-4) | Variant ID (position b37) | Nearest gene(s) | High-priority genes |
|---|---|---|---|
| Novel signals | |||
| FEV1/FVC (FVC) | rs17513135 (chr1:40,035,686) | LOC101929516 (intron) | PABPC4 |
| FEV1/FVC (FEV1) | rs6688537 (chr1:239,850,588) | CHRM3 (intron) | CHRM3 |
| FEV1/FVC (FEV1) | rs2811415 (chr3:127,991,527) | EEFSEC (intron) | RUVBL1 |
| FEV1/FVC (-) | rs13110699 (chr4:89,815,695) | FAM13A (intron) | FAM13A |
| FEV1 (FVC, FEV1/FVC) | rs3839234 (chr5:148,596,693) | ABLIM3 (intron) | GRPEL2, ABLIM3 |
| FEV1/FVC (FEV1) | rs10515750 (chr5:156,810,072) | CYFIP2 (intron) | ADAM19 |
| FEV1/FVC (FEV1) | rs200003338 (chr6:31,556,155) | LST1 (intron) | MICB*, MICA* |
| FEV1/FVC (FEV1) | rs10246303 (chr7:7,286,445) | C1GALT1 (3’ UTR) | C1GALT1 |
| FVC (FEV1) | rs10870202 (chr9:139,257,411) | DNLZ (intron) | INPP5E, CARD9 |
| FVC (FEV1) | rs7095607 (chr10:69,957,350) | MYPN (intron) | MYPN* |
| FEV1 (FVC) | rs2509961 (chr11:62,310,909) | AHNAK (intron) | ROM1, EML3, MTA2, GANAB, C11orf83* |
| FEV1/FVC (-) | rs59835752 (chr17:28,265,330) | EFCAB5 (intron) | EFCAB5, CRYBA1, SSH2, SLC6A4 |
| FEV1/FVC (FEV1) | rs11658500 (chr17:36,886,828) | CISD3 (intron) | CISD3* |
| FEV1 (FVC) | rs72448466 (chr20:62,363,640) | ZGPAT (intron) | LIME1 |
| Previously-reported signals | |||
| FEV1 (FVC) | rs6681426 (chr1:150,586,971) | MCL1/ENSA | GOLPH3L |
| FEV1/FVC (-) | rs4328080 (chr1:219,963,088) | LYPLAL1/RNU5F-1 | SLC30A10 |
| FEV1 (FVC, FEV1/FVC) | rs2571445 (chr2:218,683,154) | TNS1 (exon) | TNS1* |
| FEV1/FVC (-) | rs10498230 (chr2:229,502,503) | SPHKAP/PID1 | SPHKAP |
| FVC (FEV1) | rs1595029 (chr3:158,241,767) | RSRC1 (intron) | RSRC1 |
| FEV1 (FVC, FEV1/FVC) | rs10516526 (chr4:106,688,904) | GSTCD (intron) | INTS12, GSTCD, NPNT |
| FEV1/FVC (FEV1, FVC) | rs34712979 (chr4:106,819,053) | NPNT (intron) | NPNT |
| FEV1/FVC (FEV1) | rs138641402 (chr4:145,445,779) | GYPA/HHIP-AS1 | HHIP |
| FEV1/FVC (-) | rs153916 (chr5:95,036,700) | SPATA9/RHOBTB3 | RHOBTB3 |
| FEV1/FVC (FEV1) | rs1990950 (chr5:156,920,756) | ADAM19 (intron) | ADAM19 |
| FEV1 (FVC, FEV1/FVC) | rs34864796 (chr6:27,459,923) | ZNF184/LINC01012 | OR2B2* |
| FEV1/FVC (FEV1) | rs2857595 (chr6:31,568,469) | NCR3/AIF1 | MICB* |
| FEV1/FVC (-) | rs2070600 (chr6:32,151,443) | AGER (exon) | AGER(*) |
| FEV1 (FVC, FEV1/FVC) | rs114544105 (chr6:32,635,629) | HLA-DQB1/HLA-DQA2 | HLA-DQB1*, APOM, RNF5 |
| FEV1/FVC (FEV1) | rs113096699 (chr6:142,745,883) | GPR126 (intron) | GPR126 |
| FEV1/FVC (-) | rs148274477 (chr6:142,838,173) | GPR126/LOC153910 | GPR126* |
| FVC (FEV1) | rs10858246 (chr9:139,102,831) | QSOX2 (intron) | QSOX2 |
| FVC (FEV1) | rs2348418 (chr12:28,689,514) | CCDC91 (intron) | FLJ35252 |
| FEV1/FVC# (-) | rs11172113 (chr12:57,527,283) | LRP1 (intron) | LRP1 |
| FEV1# (-) | rs7155279 (chr14:92,485,881) | TRIP11 (intron) | ATXN3 |
| FEV1# (-) | rs117068593 (chr14:93,118,229) | RIN3 (exon) | RIN3(*) |
| FEV1/FVC (FEV1) | rs10851839 (chr15:71,628,370) | THSD4 (intron) | THSD4 |
| FEV1/FVC (-) | rs12447804 (chr16:58,075,282) | MMP15 (intron) | MMP15 |
| FEV1/FVC (FEV1) | rs3743609 (chr16:75,467,021) | CFDP1 (intron) | TMEM170A, BCAR1, CFDP1 |
| FEV1 (FVC, FEV1/FVC) | rs35524223 (chr17:44,192,590) | KANSL1 (intron) | KANSL1(*), MAPT(*), ARL17B, ARL17A, LRRC37A4, NUDT1, LRRC37A, CRHR1, LRRC37A2, ARHGAP27, FMNL1, PLEKHM1, WNT3, NSF, SPPL2C* |
| FEV1 (FVC) | rs7218675 (chr17:73,513,185) | TSEN54 (intron) | CASKIN2, TSEN54* |
| FEV1/FVC (-) | rs113473882 (chr19:41,124,155) | LTBP4 (intron) | LTBP4* |