Table 1.
Significant Colocalization of Emphysema Distribution–associated Genome-Wide Association Study Variants with Expression Quantitative Trait Loci in Lung, Blood, and Lymphoblastoid Cell Lines from the Genotype Tissue Expression Project and the COPDGene Study, Ordered by the Lead SNP Genome-Wide Association Study P Values
| Lead GWAS SNP | Chromosome | Position | HUGO Gene Annotation | GWAS P Value | eQTL Tissue | eQTL Q Value | Colocalization Probability |
|---|---|---|---|---|---|---|---|
| rs5758407 | 22 | 42076956 | MEI1 | 5.90 × 10−6 | Transformed fibroblasts (GTEx) | 4.47 × 10−18 | 0.93 |
| Lung (GTEx) | 1.59 × 10−11 | 0.91 | |||||
| Whole blood (GTEx) | 4.45 × 10−18 | 0.83 | |||||
| EBV-transformed lymphocytes (GTEx) | 2.27 × 10−6 | 0.82 | |||||
| rs7962469 | 12 | 52348259 | ACVR1B | 1.70 × 10−5 | Lung (GTEx) | 0.0005 | 0.91 |
| rs4468504 | 14 | 107122186 | IGHV3-66 | 2.70 × 10−5 | Lung (GTEx) | 6.15 × 10−18 | 0.91 |
| IGHV3-66 | Whole blood (GTEx) | 2.43 × 10−21 | 0.91 | ||||
| IGHV3-64 | Lung (GTEx) | 0.0008 | 0.89 | ||||
| IGHV4-61 | Whole blood (GTEx) | 1.52 × 10−9 | 0.87 | ||||
| IGHV3-66 | Lung (GTEx) | 6.70 × 10−8 | 0.86 | ||||
| IGHV3-64 | Whole blood (GTEx) | 2.41 × 10−6 | 0.83 | ||||
| 106666170 | IGHV1-69-2 | Whole blood (COPDGene NHW) | 3.39 × 10−18 | 0.91 | |||
| IGHV3-64 | Whole blood (COPDGene NHW) | 4.35 × 10−5 | 0.83 | ||||
| rs210611 | 6 | 117836184 | DCBLD1 | 3.90 × 10−5 | Lung (GTEx) | 0.049 | 0.82 |
Definition of abbreviations: ACVR1B = activin A receptor type 1B; COPDGene study = Genetic Epidemiology of COPD study; DCBLD1 = discoidin, CUB and LCCL domain containing 1; EBV = Epstein-Barr virus; eQTL = expression quantitative trait loci; GTEx = Genotype Tissue Expression project; GWAS = genome-wide association study; HUGO = Human Genome Organization; IGHV = immunoglobulin heavy variable; MEI1 = meiotic double-stranded break formation protein 1; NHW = non-Hispanic white individuals.
Colocalization probability is the posterior probability that the same causal variant is associated with emphysema distribution GWAS and eQTL signals. Lead SNP is the SNP with the lowest GWAS P value for association in a given GWAS-identified region. Listed are all instances for which the Bayesian colocalization results indicate that there is high posterior probability (PP4, ≥0.8) that the same causal variant is associated with emphysema distribution GWAS and eQTL signals in lung, blood, and lymphoblastoid cell lines from the GTEx project and the COPDGene study.