Table 2.
Top mitochondrial DNA copy number GWAS and selected candidate gene association hits
| SNP a | Chr | Position a | rsID | Gene Abbriviation |
Gene Nomenclature |
Location | Effect Size b |
MAF c | P-value b |
|---|---|---|---|---|---|---|---|---|---|
| Top GWAS hits | |||||||||
| chr19:51063065 d | 19 | 51063065 | rs59547719 | FOXA3 | Foxhead Box transcript | Intronic (non-coding, mRNA) | 62.2 | 0.15 | 2.2E-06 |
| rs11989281 | 8 | 134731887 | rs11989281 | NA | NA | NA | 83.1 | 0.07 | 4.4E-06 |
| rs17111633 | 10 | 101134457 | rs17111633 | CNNM1 | Cyclin mediator 1 | Intronic (non-coding, mRNA) | 151.6 | 0.02 | 6.3E-06 |
| rs16991150 | 20 | 5588410 | rs16991150 | NA | NA | NA | 201.1 | 0.01 | 1.1E-05 |
| chr19:51083059 | 19 | 51083059 | NA | MYPOP | Myb-related transcription | 3’ downstream, mRNA | 65.5 | 0.10 | 3.2E-05 |
| chr19:51005665 d | 19 | 51005665 | rs10407137 | RSPH6A | Radial spoke head 6 homolog A | Intronic (non-coding, mRNA) | 40.5 | 0.31 | 5.2E-05 |
| chr6:13154215 | 6 | 13154215 | rs11961962 | PHACTR1 | Phosphatase and actin regulator 1 | Intronic (non-coding, mRNA) | 82.1 | 0.05 | 9.3E-05 |
| rs6939784 d | 6 | 103603097 | rs6939784 | LOC105377914 | Contig mRNA transcript | NA | −40.7 | 0.30 | 9.9E-05 |
| chr19:51059105 d | 19 | 51059105 | rs10410870 | FOXA3 | Foxhead Box transcript | 5’ upstream, mRNA | 38.5 | 0.32 | 1.1E-04 |
| rs6941513 d | 6 | 163950790 | rs6941513 | NA | NA | NA | 35.9 | 0.40 | 1.2E-04 |
| rs9855301 | 3 | 119416106 | rs9855301 | NA | NA | NA | 69.7 | 0.08 | 1.2E-04 |
| rs12513009 d | 4 | 90774543 | rs12513009 | LOC105377329 | NA | Intronic (non-coding, mRNA) | −41.1 | 0.27 | 1.2E-04 |
| rs17184588 d | 1 | 24238099 | rs17184588 | NA | NA | NA | 36.4 | 0.31 | 1.2E-04 |
| rs13017599 | 2 | 61017835 | rs13017599 | NA | NA | NA | −59.1 | 0.10 | 1.3E-04 |
| rs7745161 d | 6 | 163949460 | rs7745161 | NA | NA | NA | 36.6 | 0.41 | 1.3E-04 |
| rs1008295 d | 6 | 163530086 | rs1008295 | PACRG | Parkin coregulated gene | Intronic (non-coding, mRNA) | 35.0 | 0.37 | 1.7E-04 |
| rs10519453 | 4 | 139432369 | rs10519453 | SLC7A11 | Solute carrier family 7 (anionic amino acid transporter light chain, xc-system) | Intronic (non-coding, mRNA) | 52.0 | 0.13 | 1.9E-04 |
| rs6467991 | 7 | 83792673 | rs6467991 | SEMA3A | Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A | Intronic (non-coding, mRNA) | 75.0 | 0.06 | 2.0E-04 |
| chr6:13108480 | 6 | 13108480 | ENSSNP8230549 | PHACTR1 | NA | Intronic (non-coding, mRNA) | 82.7 | 0.05 | 2.0E-04 |
| chr6:13095627 | 6 | 13095627 | rs4715043 | PHACTR1 | Phosphatase and actin regulator 1 | Intronic (non-coding, mRNA) | 62.0 | 0.10 | 2.0E-04 |
| Selected MB and OP Candidate SNPs | |||||||||
| rs2279238 | 11 | 47238600 | rs2279238 | NR1H3 | Liver X receptor, alpha|liver X receptor-alpha | Coding mRNA | 17.7 | 0.32 | 7.2E-02 |
| rs627297 | 11 | 77441437 | rs627297 | NDUFC2_KCTD14 | NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2, 14.5kDa | Intronic (non-coding, mRNA) | −23.8 | 0.17 | 5.2E-02 |
| chr3:12340308 | 3 | 12340308 | NA | PPARG | Peroxisome proliferator-activated receptor gamma | Intronic (non-coding, mRNA) | −24.8 | 0.26 | 2.6E-02 |
| rs7131938 | 12 | 52059194 | rs7131938 | SP1 | Sp1 transcription factor | 5’ upstream mRNA | −25.2 | 0.21 | 3.7E-02 |
a
NCBI build 36.1 hg18 assembly;
b
Linear regression estimates of SNPs in relation to mtDNA copy number adjusted for placental abruption status and first two principal components;
c
Minor Allele Frequency;
d
Selected top GWAS SNPs for wGRS analysis