Table 2. Significant associations between nuclear genetic variants and the expression levels of genes encoded in the mitochondrial genome that replicate in independent tissue matched datasets.
Point-wise permutation P values were generated by extrapolating from the underlying beta distribution (see Materials and methods).
| Tissue | Peak nuclear SNP |
Chr | Position | A1 | MAF | MT gene |
P value |
P value (FDR corrected) |
P value (Point-wise Permutation) |
Beta | Replication P value | Replication beta |
Nuclear gene annotation |
Nuclear SNP annotation |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LCLs | rs10205130 | 2 | 44151572 | C | 0.426 | MTND1 | 1.23E-10 | 6.40E-05 | 1.18E-10 | 0.023 | 5.70E-05 | 0.015 | LRPPRC | Intronic |
| Whole Blood |
rs10172506 | 2 | 55865469 | C | 0.062 | MTND5 | 4.40E-40 | 2.00E-33 | 1.39E-39 | 0.058 | 2.00E-08 | 0.037 | PNPT1 | Intronic |
| Whole Blood |
rs7558127 | 2 | 55866605 | G | 0.064 | MTND6 | 5.26E-32 | 8.30E-26 | 5.29E-32 | 0.070 | 8.70E-07 | 0.043 | PNPT1 | Intronic |
| LCLs | rs2627775 | 2 | 55877113 | T | 0.458 | MTCO1 | 1.33E-09 | 4.10E-04 | 9.95E-10 | 0.017 | 6.30E-04 | 0.013 | PNPT1 | Intronic |
| LCLs | rs62165226 | 2 | 55878339 | C | 0.484 | MTCO3 | 2.79E-08 | 7.60E-03 | 2.71E-08 | −0.018 | 6.80E-06 | −0.018 | PNPT1 | Intronic |
| Whole Blood |
rs6973982 | 7 | 45143892 | G | 0.148 | MTCO2 | 7.53E-31 | 8.60E-25 | 1.12E-30 | −0.028 | 2.30E-08 | −0.023 | TBRG4 | Intronic |
| Whole Blood |
rs6973982 | 7 | 45143892 | G | 0.148 | MTCO3 | 1.23E-25 | 6.40E-20 | 1.05E-25 | −0.028 | 1.40E-04 | −0.019 | TBRG4 | Intronic |
| Skin (Not sun exposed) |
rs2304693 | 7 | 45148667 | A | 0.201 | MTCO3 | 2.84E-12 | 2.10E-05 | 2.93E-12 | −0.027 | 1.80E-03 | −0.026 | TBRG4 | Missense |
| Whole Blood |
rs2304694 | 7 | 45148773 | A | 0.148 | MTND1 | 2.34E-17 | 6.10E-12 | 3.19E-17 | 0.015 | 1.60E-08 | 0.024 | TBRG4 | Missense |
| LCLs | rs2304694 | 7 | 45148773 | A | 0.197 | MTND4 | 2.35E-18 | 3.90E-11 | 2.22E-18 | −0.029 | 1.40E-04 | −0.019 | TBRG4 | Missense |
| Subcutaneous Adipose |
rs12579998 | 12 | 27861446 | G | 0.174 | MTND1 | 2.48E-23 | 6.50E-17 | 1.09E-23 | −0.032 | 3.20E-05 | −0.032 | - | Intergenic |
| Subcutaneous Adipose |
rs12579998 | 12 | 27861446 | G | 0.174 | MTND4 | 2.20E-12 | 1.70E-06 | 1.56E-12 | −0.022 | 4.00E-04 | −0.027 | - | Intergenic |
| Skin (Not sun exposed) |
rs11049103 | 12 | 27862081 | A | 0.179 | MTND1 | 7.72E-12 | 2.10E-05 | 6.68E-12 | −0.022 | 8.10E-04 | −0.026 | - | Intergenic |
| Whole Blood |
rs74863981 | 20 | 3109875 | A | 0.099 | MTCO1 |
4.24E-11 | 5.40E-06 | 5.25E-11 | −0.024 | 6.60E-05 | −0.022 | UBOX5 | Intronic |