Table 3.
Association of variants in the region of chromosome 17 between 35.0 and 35.5 Mb (around 17q21) with expression quantitative traits for local genes in 875 children
| Nearby gene | SNP a | ORMDL3 expression (r2) b | pc | Other eQTLd | expression (r2) b | pc |
|---|---|---|---|---|---|---|
|
Region between 35.0 and 35.2 Mb
| ||||||
| PNMT | rs876493 | 0.05 | 3.38×10−8 | IKZF3 | 0.05 | 6.28×10−8 |
| GSDML | 0.05 | 4.50×10−7 | ||||
|
| ||||||
| PERLD1 | rs2941504 | 0.05 | 6.10×10−9 | IKZF3 | 0.08 | 1.47×10−14 |
| GSDML | 0.05 | 5.37×10−7 | ||||
|
| ||||||
| ERBB2 | rs2952155 | 0.05 | 2.48×10−8 | IKZF3 | 0.43 | 4.08×10−11 |
| GSDML | −0.33 | 1.93×10−5 | ||||
|
| ||||||
|
Region between 35.2 and 35.4 Mb
| ||||||
| IKZF3 | rs9303277 | 0.20 | 1.39×10−44 | IKZF3 | 0.13 | 2.53×10−27 |
| ZPBP2 | 0.02 | 0.04 | ||||
| GSDML | 0.19 | 6.09×10−44 | ||||
|
| ||||||
| ZPBP2 | rs11557467 | 0.20 | 6.75×10−45 | IKZF3 | 0.13 | 1.78×10−26 |
| ZPBP2 | 0.02 | 0.09 | ||||
| GSDML | 0.20 | 3.64×10−45 | ||||
|
| ||||||
| GSDML | rs2305480 | 0.16 | 1.78×10−35 | IKZF3 | 0.07 | 1.15×10−12 |
| GSDML | 0.17 | 6.33×10−36 | ||||
|
| ||||||
| ORMDL3 | rs8076131 | 0.16 | 4.05×10−34 | IKZF3 | 0.07 | 4.86×10−12 |
| GSDML | 0.16 | 4.03×10−33 | ||||
|
| ||||||
| GSDM1 | rs3902025 | 0.10 | 1.40×10−19 | IKZF3 | 0.02 | 0.02 |
| GSDML | 0.10 | 1.83×10−20 | ||||
| MED24 | 0.02 | 0.46 | ||||
|
| ||||||
|
Region between 35.4 and 35.5 Mb
| ||||||
| PSMD3 | rs2227321 | 0.05 | 2.79×10−7 | GSDML | 0.04 | 0.001 |
| MED24 | 0.02 | 0.20 | ||||
|
| ||||||
| CSF3 | rs1042658 | 0.03 | 0.001 | GSDML | 0.03 | 0.001 |
| MED24 | 0.07 | 2.62×10−12 | ||||
|
| ||||||
| MED24 | rs8065443 | 0.04 | 2.59×10−5 | GSDML | 0.05 | 3.77×10−7 |
| MED24 | 0.05 | 3.84×10−8 | ||||
SNP near each gene with the smallest overall p-value from primary analyses with wheeze phenotypes (Table 2) and their relationships with expression quantitative traits for genes in the ORMDL3 region of chromosome 17. Supplemental Table A6 shows the complete list of expression quantitative traits for the SNPs reported in this table. A complete list of SNPs and their relationship with expression quantitative traits for all loci in this region is available from the authors.
r2 refers to variance in expression explained in expression levels by SNP. For all results, 875 samples were available with both genotype and expression data.
Bonferroni corrected p values (based on 3855 tests)
Other eQLT, results are shown where evidence for association exceeds a threshold when taking a Bonferroni corrected p value for 3855 tests (257 independent loci*15 expression quantitative traits). All raw p values are <0.0002.