Table 1.
Forty eight genes with a significant (FDR < 5%) association with asthma risk in the Ferreira et al.14 GWAS.
| Gene | Position | N eQTLs | N eQTLs tested | N eQTLs with P<0.05 | Best individual eQTL
|
EUGENE P-value | Potential novel associationa | |
|---|---|---|---|---|---|---|---|---|
| SNP | P-value | |||||||
| HLA-DQB1 | 6:32627244 | 78 | 26 | 15 | rs1063355 | 1.8 × 10−13 | <10−6 | No |
| GSDMB | 17:38060848 | 15 | 11 | 5 | rs2952140 | 1.2 × 10−8 | < 10−6 | No |
| LIMS1 | 2:109150857 | 15 | 14 | 4 | rs1063355 | 1.8 × 10−13 | < 10−6 | No* |
| TLR1 | 4:38792298 | 9 | 6 | 3 | rs12233670 | 1.4 × 10−11 | <10−6 | No |
| ORMDL3 | 17:38077294 | 19 | 14 | 5 | rs2952140 | 1.2 × 10−8 | <10−6 | No |
| IKZF3 | 17:37921198 | 9 | 7 | 3 | rs7207600 | 4.5 × 10−7 | < 10−6 | No |
| IL18RAP | 2:103035149 | 18 | 16 | 6 | rs13018263 | 5.0 × 10−6 | <10−6 | No |
| CLEC16A | 16:11038345 | 4 | 4 | 2 | rs35441874 | 2.9 × 10−8 | <10−6 | No |
| ZPBP2 | 17:38024417 | 2 | 2 | 1 | rs9916765 | 1.9 × 10−9 | <10−6 | No |
| GRB7 | 17:37894180 | 2 | 1 | 1 | rs14050 | 1.4 × 10−7 | <10−6 | No |
| TINF2 | 14:24708849 | 4 | 4 | 2 | rs3135006 | 1.7 × 10−6 | < 10−6 | No* |
| TAP2 | 6:32789610 | 48 | 36 | 11 | rs2858312 | 1.9 × 10−5 | 2.0 × 10−6 | No |
| TAP1 | 6:32812986 | 13 | 12 | 4 | rs6928482 | 2.0 × 10−8 | 2.0 × 10−6 | No |
| HSPA1B | 6:31795512 | 13 | 13 | 6 | rs13215091 | 4.7 × 10−4 | 2.0 × 10−6 | No |
| TSLP | 5:110405760 | 6 | 6 | 4 | rs17132582 | 3.2 × 10−4 | 2.0 × 10−6 | No |
|
| ||||||||
| DYNC1H1 | 14:102430865 | 6 | 5 | 2 | rs4906262 | 1.1 × 10−5 | 2.0 × 10−6 | Yes |
|
| ||||||||
| HLA-DRB1 | 6:32546546 | 97 | 46 | 18 | rs3806156 | 1.4 × 10−4 | 4.0 × 10−6 | No |
| IL18R1 | 2:102927989 | 11 | 11 | 5 | rs6751967 | 3.2 × 10−6 | 4.0 × 10−6 | No |
| SOCS1 | 16:11348262 | 7 | 6 | 5 | rs7184491 | 3.5 × 10−6 | 4.0 × 10−6 | No |
| CISD3 | 17:36886488 | 4 | 4 | 2 | rs2941503 | 1.6 × 10−7 | 5.0 × 10−6 | No |
| PGAP3 | 17:37827375 | 2 | 2 | 1 | rs903502 | 1.5 × 10−6 | 6.0 × 10−6 | No |
| IL1RL2 | 2:102803433 | 2 | 2 | 1 | rs9646944 | 6.7 × 10−7 | 9.0 × 10−6 | No |
| CLK3 | 15:74890841 | 2 | 2 | 1 | rs9268853 | 1.8 × 10−6 | 9.0 × 10−6 | No* |
| SMAD3 | 15:67356101 | 7 | 7 | 2 | rs17293632 | 2.0 × 10−7 | 1.1 × 10−5 | No |
| SAFB | 19:5623046 | 2 | 2 | 1 | rs9268853 | 1.8 × 10−6 | 1.1 × 10−5 | No* |
|
| ||||||||
| P2RY13 | 3:151044100 | 8 | 8 | 5 | rs9877416 | 1.2 × 10−4 | 1.2 × 10−5 | Yes |
|
| ||||||||
| AOAH | 7:36552456 | 26 | 21 | 3 | rs9268853 | 1.8 × 10−6 | 1.3 × 10−5 | No* |
| SLC44A4 | 6:31830969 | 2 | 2 | 1 | rs9275141 | 1.1 × 10−6 | 1.3 × 10−5 | No |
| STARD3 | 17:37793318 | 7 | 3 | 1 | rs2941503 | 1.6 × 10−7 | 1.5 × 10−5 | No |
| LTA | 6:31539831 | 16 | 13 | 5 | rs2442752 | 1.5 × 10−5 | 1.6 × 10−5 | No |
| MED24 | 17:38175350 | 5 | 5 | 2 | rs7502514 | 4.8 × 10−5 | 1.7 × 10−5 | No |
|
| ||||||||
| HIBADH | 7:27565061 | 14 | 12 | 6 | rs6951856 | 9.6 × 10−5 | 2.9 × 10−5 | Yes |
| P2RY12 | 3:151055168 | 6 | 6 | 4 | rs17282940 | 7.0 × 10−5 | 3.0 × 10−5 | Yes |
|
| ||||||||
| NR1D1 | 17:38249040 | 5 | 4 | 2 | rs12150298 | 2.8 × 10−6 | 3.0 × 10−5 | No |
| ZNF707 | 8:144766622 | 9 | 8 | 3 | rs17609240 | 1.5 × 10−6 | 4.2 × 10−5 | No* |
| TOP2A | 17:38544768 | 1 | 1 | 1 | rs2102928 | 4.1 × 10−5 | 4.9 × 10−5 | No |
| HLA-DRB6 | 6:32520490 | 60 | 13 | 6 | rs522254 | 6.3 × 10−4 | 5.4 × 10−5 | No |
|
| ||||||||
| REEP3 | 10:65281123 | 6 | 4 | 2 | rs7898489 | 9.1 × 10−6 | 6.1 × 10−5 | Yes |
| PTCSC3 | 14:36605314 | 2 | 2 | 2 | rs7148603 | 1.8 × 10−4 | 6.5 × 10−5 | Yes |
| P2RY14 | 3:150929905 | 13 | 12 | 5 | rs10513393 | 1.1 × 10−4 | 7.2 × 10−5 | Yes |
|
| ||||||||
| HLA-DQA1 | 6:32595956 | 79 | 29 | 9 | rs504594 | 1.7 × 10−5 | 8.1 × 10−5 | No |
|
| ||||||||
| ACO2 | 22:41865129 | 3 | 3 | 2 | rs960596 | 1.3 × 10−4 | 9.4 × 10−5 | Yes |
|
| ||||||||
| HCP5 | 6:31368479 | 23 | 22 | 4 | rs2071595 | 6.7 × 10−6 | 9.6 × 10−5 | No |
| NEU1 | 6:31825436 | 8 | 8 | 5 | rs9267901 | 9.1 × 10−4 | 9.8 × 10−5 | No |
| MICB | 6:31462658 | 41 | 30 | 9 | rs9268764 | 3.3 × 10−5 | 1.2 × 10−4 | No |
|
| ||||||||
| B4GALT3 | 1:161141100 | 10 | 9 | 3 | rs1668873 | 1.5 × 10−3 | 1.2 × 10−4 | Yes |
| USMG5 | 10:105148798 | 16 | 14 | 4 | rs1163073 | 4.9 × 10−4 | 1.5 × 10−4 | Yes |
| F12 | 5:176829141 | 3 | 3 | 2 | rs4976765 | 1.7 × 10−3 | 1.5 × 10−4 | Yes |
a
Potential novel genetic associations with asthma (highlighted in grey) are those for which the gene-based association was not driven by eQTLs located in known allergy risk loci. Known allergy loci are defined as those that contain a variant reported to be associated with asthma or other allergic diseases with P<5×10−8 in published GWAS.
*
Genes not located in an asthma risk locus but for which the gene-based association was driven by trans-eQTLs in LD with allergy risk variants (see Table E7 for more details).