Table I.
Association of CSTA Genotypes with CSTA Gene Expression in the Small Airway Epithelium1
| SNP identity3 | Chr. 3 location4 | Minor allele frequency5 | p value for association of genotype with expression level2 |
|||
|---|---|---|---|---|---|---|
| Assessed by microarray
| ||||||
| All subjects6 (n=112) | Healthy nonsmokers (n=44) | Healthy smokers (n=48) | COPD smokers (n=20) | |||
| rs1354162 | 123,436,767 | 0.040 | 0.02 | NS | NS | 4.6 × 10−3 |
| rs7652858 | 123,480,795 | 0.125 | 3.6 × 10−3 | NS | NS | NS |
| rs2134225 | 123,484,943 | 0.125 | 3.6 × 10−3 | NS | NS | NS |
| rs16832956 | 123,500,198 | 0.161 | 4.5 × 10−4 | NS | 3.4 × 10−3 | 0.010 |
| rs1402200 | 123,505,107 | 0.411 | 7.3 × 10−3 | NS | NS | NS |
| rs5008830 | 123,513,152 | 0.089 | 1.0 × 10−3 | 0.025 | 1.1 × 10−5 | 0.038 |
| rs2001548 | 123,515,479 | 0.101 | 1.7 × 10−3 | NS | 3.4 × 10−5 | 0.038 |
| rs4678180 | 123,520,487 | 0.455 | 5.2 × 10−3 | NS | NS | NS |
| rs9864290 | 123,522,752 | 0.451 | 7.8 × 10−3 | NS | NS | NS |
| rs6803098 | 123,523,300 | 0.453 | 4.1 × 10−3 | NS | NS | NS |
| rs9817571 | 123,538,670 | 0.099 | 0.03 | NS | 0.018 | NS |
| rs9842752 | 123,539,553 | 0.076 | 0.03 | NS | NS | NS |
CSTA gene expression levels in small airway epithelium as assessed by Affymetrix HGU133 Plus 2.0 microarray expression probe set 204971_at were correlated with Affymetrix Human SNP Array 5.0 cis-SNPs situated within 100 kbp of the CSTA gene location on chromosome 3.3q21.
For analysis with the group of all subjects, p values represent Wald statistic following permutation analysis: after initial associations were identified, each association was further tested by performing 103 permutations within clusters of similar genetic ancestry, as defined by STRUCTURE, using PLINK software. For the subgroup analyses, t-tests are shown.
Only those SNPs with p values for association of genotype with expression of <0.05 are shown. SNPs are listed in ascending order of location on chromosome 3. 5′ to 3′, the first 4 SNPs listed are within introns of the upstream CASR gene, the next 6 are intergenic, and the last 2 listed SNPs are located within introns of CSTA.
Ch, chromosome. Locations refer to NCBI Human Genome Reference Genome Assembly, Build 36.3
Minor allele frequencies observed in the study population.
All subjects with SAE gene expression data and genotype data. Healthy nonsmokers (n=44), healthy smokers (n=48) and COPD smokers (n=20) combined. NS=not significant (p>0.05).