Table 4 Association of COPD-SNPs with transcriptome-wide gene expression in lungs (N = 1087)
From: Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics
SNP | Tested allele | Probe | Chr | Position (hg19) | Annotation | β | SE | P |
|---|---|---|---|---|---|---|---|---|
rs12914385 CHRNA3 intronic variant chr15:g.78606381C>T | T | 100154936_TGI_ata | 15 | 78792408-78792890 | 3’UTR IREB2 (AF147302) | 0.23002 | 0.0091 | 2.13 × 10 −142 |
100148404_TGI_at | 15 | 78832747-78841563 | PSMA4 (NM_002789) | −0.06463 | 0.0058 | 1.62 × 10 −28 | ||
100156434_TGI_at | 15 | 78857862-78887611 | CHRNA5 (NM_000745) | 0.13973 | 0.0139 | 1.00 × 10 −23 | ||
100313804_TGI_at | 15 | 78828532-78828986 | mRNA intron HYKK (AA532820) | −0.09604 | 0.0152 | 2.38 × 10 −10 | ||
100132425_TGI_at | 15 | 78799906-78829715 | HYKK (NM_001083612) | 0.082 | 0.0147 | 2.56 × 10 −8 | ||
100123649_TGI_at | 15 | 78887647-78913637 | CHRNA3 (NM_000743) | 0.11452 | 0.0255 | 7.25 × 10 −6 | ||
rs8034191 HYKK intronic variant chr15:g.78513681T>C | C | 100154936_TGI_ata | 15 | 78792408-78792890 | 3’UTR IREB2 (AF147302) | −0.2436 | 0.0084 | 3.27 × 10 −184 |
100148404_TGI_at | 15 | 78832747-78841563 | PSMA4 (NM_002789) | 0.0719 | 0.0056 | 3.17 × 10 −37 | ||
100156434_TGI_at | 15 | 78857862-78887611 | CHRNA5 (NM_000745) | −0.1594 | 0.0136 | 9.11 × 10 −32 | ||
100313804_TGI_at | 15 | 78828532-78828986 | mRNA intron HYKK (AA532820) | 0.1108 | 0.0149 | 9.15 × 10 −14 | ||
100132425_TGI_at | 15 | 78799906-78829715 | HYKK (NM_001083612) | −0.1009 | 0.0145 | 2.90 × 10 −12 | ||
100146326_TGI_at | 3 | 31745705-31763038 | OSBPL10 (BX103488) | 0.0491 | 0.011 | 7.57 × 10 −6 | ||
100312267_TGI_at | 15 | 78887350-78889074 | CHRNA3 (AJ584709) | −0.0901 | 0.0203 | 9.42 × 10 −6 | ||
100123649_TGI_at | 15 | 78887647-78913637 | CHRNA3 (NM_000743) | −0.108 | 0.0253 | 2.02 × 10 −5 | ||
100158626_TGI_at | 4 | 89658713-89659241 | mRNA intron FAM13A (AI922966) | −0.0632 | 0.015 | 2.37 × 10 −5 | ||
100143446_TGI_at | 15 | 78730518-78793798 | IREB2 (NM_004136) | −0.0259 | 0.0062 | 2.76 × 10 −5 | ||
rs13180 IREB2 synonymous variant chr15:g.78497146C>T | T | 100154936_TGI_ata | 15 | 78792408-78792890 | 3’UTR IREB2 (AF147302) | −0.2046 | 0.0097 | 3.17 × 10 −98 |
100129239_TGI_at | 15 | 78780991-78786607 | IREB2 (AW118658) | 0.059 | 0.0114 | 2.46 × 10 −7 | ||
100143446_TGI_at | 15 | 78730518-78793798 | IREB2 (NM_004136) | −0.0309 | 0.0064 | 1.41 × 10 −6 | ||
100161812_TGI_at | 2 | 242943360-242948160 | (AK126530) | −0.0381 | 0.0086 | 8.78 × 10 −6 | ||
100140544_TGI_at | 14 | 104145786-104168220 | KLC1 (CO247613) | 0.0422 | 0.0095 | 9.38 × 10 −6 | ||
100144578_TGI_at | 2 | 37869087-37871279 | UTR CDC42EP3 (AK055915) | −0.0428 | 0.0099 | 1.44 × 10 −5 | ||
100141776_TGI_at | 13 | 50571143-50592603 | TRIM13 (NM_052811) | 0.0412 | 0.0098 | 2.83 × 10 −5 | ||
rs8042238 IREB2 intronic variant chr15:g.78481929C>T | T | 100154936_TGI_ata | 15 | 78792408-78792890 | 3’UTR IREB2 (AF147302) | −0.2049 | 0.0097 | 1.10 × 10 −98 |
100129239_TGI_at | 15 | 78780991-78786607 | IREB2 (AW118658) | 0.0587 | 0.0114 | 2.84 × 10 −7 | ||
100143446_TGI_at | 15 | 78730518-78793798 | IREB2 (NM_004136) | −0.0312 | 0.0064 | 1.09 × 10 −6 | ||
100161812_TGI_at | 2 | 242943360-242948160 | (AK126530) | −0.0389 | 0.0086 | 5.73 × 10 −6 | ||
100140544_TGI_at | 14 | 104145786-104168220 | KLC1 (CO247613) | 0.0423 | 0.0095 | 8.79 × 10 −6 | ||
100144578_TGI_at | 2 | 37869087-37871279 | UTR CDC42EP3 (AK055915) | −0.0429 | 0.0099 | 1.36 × 10 −5 | ||
100141776_TGI_at | 13 | 50571143-50592603 | TRIM13 (NM_052811) | 0.0415 | 0.0098 | 2.47 × 10 −5 |
