Table 5.
Co-localization results for lung function measures and cognitive traits
| Gene | Lung function trait | Cognitive trait | Highest PP | SNP | Linkage disequilibrium (R2) |
|---|---|---|---|---|---|
| CSNK2B | FEV1/FVC | Fluid intelligence | H4: 0.976 | rs9267531 | |
| Pairs matching | H4: 0.911 | rs9267531 | |||
| FVC | Fluid intelligence | H4: 0.995a | rs9267531 | ||
| H3: 0.948a | rs3117578 & rs9267531 | 0.02 | |||
| Pairs matching | H4: 0.946a | rs9267531 | |||
| H3: 0.941a | rs3117578 & rs9267531 | 0.02 | |||
| NFATC3 | FEV1/FVC | Fluid intelligence | H4: 0.802a | rs548092276 & rs11275011 | 0.85b |
| ITGAV | FEV1/FVC | Pairs matching | H4: 0.678 | rs2084448c | |
| KAT8 | FVC | Pairs matching | H4: 0.829 | rs138259061 | |
| Alzheimer’s diseased | H3: 0.989 | rs1978487, rs11865499e | 0.23 | ||
| PTCH1 | FVC | Reaction time | H3: 0.960a | rs113154802, rs539078574 | 0.13 |
| Fluid intelligence | H3: 0.999a | rs113154802, rs28496034 | 0.19 | ||
| FEV1/FVC | Reaction time | H4: 0.527a | rs2297086 & rs539078574 | 0.54 | |
| H3: 0.960a | rs75614054, rs539078574 | 0.13 | |||
| Fluid intelligence | H3: 0.601a | rs2297086, rs28496034 | 0.86 | ||
| H3: 0.999a | rs75614054, rs28496034 | 0.19 | |||
| SERPINC1 | FVC | Reaction time | H3: 0.612a | rs2227603, rs2227592 | 0.003 |
Highlighted in bold are variants with evidence for co-localization where the variants for each trait in the co-localization pair were either the same (a high gene PP.H4 and a high SNP PP.H4: variants in CSNK2B1 and KAT8) or distinct but with correlated signals (high SNP PP.H4 for the pair by coloc-SuSiE: variants in NFATC3 and PTCH1 separated by ‘&’).
aBy SuSiE-coloc.
bVariants rs548092276 and rs11275011 are not in 1000G reference panel (GRCh37 and GRCh38), so R2 is reported based on data for the two variants in UKB.
cSNP PP.H4 = 18.8% (the highest reported for variants in ITGAV), not large enough to form a co-localization case.
dFrom GWAS meta-analysis.
eVariants detected by fine mapping (the highest PP) as SuSiE did not operate for KAT8.