Table 3. Loci associated with mean MtHz.
The positions (GRCh37/hg19 assembly) are ordered by P value, and those exceeding genome-wide significance are provided. The SNP with the smallest P value in each interval is given. Beta values are the per-allele effect of the B allele upon natural log mean MtHz value.
| Chromosome | Position | SNP | Alleles (A/B) | BAF | Beta | 95% CI | P |
Nearest gene(s) |
Nearest gene function |
| 10q21.1 | 60,155,120 | rs1049432 | G/T | 0.183 | 0.035 | 0.033–0.037 | 2 × 10–223 |
TFAM | mtDNA packaging factor |
| 6p21.32 | 32,626,574 | rs28539606 | A/G | 0.147 | 0.020 | 0.016–0.024 | 4 × 10–23 |
HLA-DQB1 | Immune response |
| Xp22.3 | 1,413,667 | rs28602228 | C/T | 0.371 | 0.008 | 0.006–0.010 | 8.4 × 10–16 |
CSF2RA | Signal transduction |
| 2q13 | 113,876,498 | rs4251979 | C/T | 0.733 | −0.008 | −0.010 to −0.006 |
1.2 × 10–15 |
IL1RN | Viral response |
| 3p14.3 | 58,302,935 | rs73081554 | C/T | 0.068 | −0.014 | −0.018 to −0.010 |
3.2 × 10–14 |
RPP14 | Nuclear ribonuclease P component |
| 19p13.3 | 5,555,098 | rs12461806 | A/G | 0.913 | −0.012 | −0.015 to −0.009 |
1.8 × 10–13 |
TINCR | Noncoding RNA |
| 19q13.2 | 39,737,576 | rs370209610 | C/T | 0.981 | −0.023 | −0.029 to −0.016 |
6.3 × 10–13 |
IFNL4 | Viral response |
| 10q24.31 | 102,764,338 | rs58678340 | C/T | 0.014 | −0.026 | −0.033 to −0.018 |
3.2 × 10–12 |
TWNK/ MRPL43 |
mtDNA helicase/ mitoribosome |
| 15q21.3 | 54,107,732 | rs200605061 | D/I | 0.121 | 0.009 | 0.007–0.012 | 6.9 × 10–12 |
WDR72 | Regulator of membrane shape |
| 13q22.1 | 73,690,621 | rs7319964 | A/T | 0.539 | −0.006 | −0.008 to −0.004 |
7.4 × 10–12 |
KLF5 | Nuclear DNA binding factor |
| 20p12.3 | 7,014,445 | rs2149642 | C/T | 0.775 | 0.007 | 0.005–0.009 | 1.5 × 10–11 |
BMP2 | Bone morphogenetic protein |
| 7p22.1 | 6,933,726 | rs143803034 | A/G | 0.961 | −0.015 | −0.019 to −0.011 |
1.8 × 10–11 |
CCZ1B | Vacuolar fusion protein |
| 5q11.2 | 52,832,775 | rs10063311 | C/G | 0.224 | −0.006 | −0.008 to −0.004 |
9.4 × 10–10 |
NDUFS4 | Structural component of complex I |
| 2p11.2 | 87,831,354 | rs145232625 | C/T | 0.257 | −0.006 | −0.008 to −0.004 |
2.0 × 10–9 |
PLGLB2 | Plasminogen like protein |
| 10q23.32 | 93,306,966 | rs4933661 | C/G | 0.356 | 0.005 | 0.004–0.007 | 2.2 × 10–9 |
HECTD2 | Ubiquitin ligase |
| 16p13.13 | 11,143,355 | rs758049676 | D/I | 0.432 | 0.005 | 0.003–0.007 | 4.1 × 10–9 |
CLEC16A | Promoter of antigen presentation |
| 5q32 | 149,579,857 | rs2286639 | A/G | 0.208 | −0.006 | −0.008 to −0.004 |
1.0 × 10–8 |
SLC6A7 | Neurotransmitter transport |
| 12q24.23 | 120,146,925 | rs11064881 | A/G | 0.926 | −0.009 | −0.012 to −0.006 |
1.4 × 10–8 |
CIT/PRKAB1 | Ser-Thr kinase/ AMP-kinase subunit |
| 19q13.33 | 49,206,462 | rs681343 | C/T | 0.484 | 0.005 | 0.003–0.006 | 2.0 × 10–8 |
FUT2/ MAMSTR |
Fucosyltransferase/ transcription factor |
| 2p13.2 | 72,256,404 | rs11679052 | C/G | 0.578 | −0.005 | −0.006 to −0.003 |
5.0 × 10–8 |
CYP26B1 | Retinoic acid metabolism |