Table 4.
Proxy QTNs in linkage disequilibrium (LD) with significantly-associated MetS QTNs
| Ethnic group | Trait | QTN significantly associated with trait in Table 2 | Proxy QTN (rsid) | CHR | bp (GRCh37) | Distance (bp) | MAF (%)a | r2 (LD) | Correlated alleles (significant QTN = proxy QTN) | RegulomeDBb | Gene: function | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Significant QTN (rsid) | Gene: function | |||||||||||
| AA | log(TG) | rs114606502 | TMEM132D: intronic | rs142863227 | 12 | 130,094,067 | 23,285 | 0.4 | 1 |
T = G C = C |
4 | TMEM132D: intronic |
| rs116163662 | 12 | 130,114,869 | 2483 | 0.5 | 0.83 |
T = G C = A |
3a | TMEM132D: intronic | ||||
| EA | log(TG) | rs1260326 | GCKR: exonic, Nonsynonymous | rs780094 | 2 | 27,741,237 | 10,297 | 41 | 0.91 |
T = T C = C |
2c | GCKR: intronic |
| JA | Weight | rs2302308, rs74398478, rs17051338, rs77438622, rs77006299 | QRFPR: intronic | rs55975435 | 4 | 122,254,014 | 6028 | 12 | 0.98 |
T = A G = G |
7 | QRFPR: exonic, synonymous |
AA African Americans, EA European Americans, JA Japanese Americans, MA Mexican Americans
aMinor allele frequency (MAF) from 1000G corresponding reference group: AFR (for AA GENNID), EAS (for JA GENNID), EUR (for EA GENNID)
bRegulomeDB rank is defined by the following supporting data for evidence of regulatory effects: 2c: TF binding + matched TF motif + DNase peak; 3a: TF binding + any motif + DNase peak; 4: TF binding + DNase peak; 7: other; see https://www.regulomedb.org/regulome-help/