Table 2.
GWAS meta-analysis of DNAmTL derived from participants of European Ancestry and African Ancestry.
| SNP | CHR | BP | Effect allelea | META | EA | AA | Gene or nearest gene | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| BETA (EFFECT) | Meta P-value | P (I2) | MAF (MA) | Association P-value | MAF(MA) | Association P-value | |||||
| Genotyped SNPs (p < 1 × 10−5) | |||||||||||
| rs4374022 | 12 | 55,373,780 | C | −0.058 | 3.87E−08 | 0.81(0) | 0.22(T) | 0.00014 | 0.48 (T) | 0.00012 | TESPA1 |
| rs3759165 | 12 | 55,367,715 | C | −0.054 | 2.23E−07 | 0.63 (0) | 0.22 (T) | 0.00016 | 0.46 (C) | 0.0005 | TESPA1 |
| rs2147317 | 1 | 68,990,012 | C | −0.052 | 1.17E−06 | 0.65 (0) | 0.35 (C) | 0.00058 | 0.25 (C) | 0.00072 | DEPDC1-AS1 |
| rs8128746 | 21 | 19,656,171 | C | −0.049 | 1.84E−06 | 0.61 (0) | 0.43 (C) | 9.24E-05 | 0.28 (C) | 0.0073 | TMPRSS15 |
| rs7297842 | 12 | 55,404,523 | A | −0.050 | 3.25E−06 | 0.36 (0) | 0.21 (G) | 0.00017 | 0.47 (A) | 0.0051 | TESPA1; NEUROD4 |
| rs842192 | 1 | 1.78E + 08 | C | −0.055 | 4.47E−06 | 0.99 (0) | 0.13 (A) | 0.0082 | 0.34 (A) | 0.0002 | SEC16B |
| rs3776566 | 5 | 36,631,733 | G | −0.061 | 5.48E−06 | 0.75 (0) | 0.05 (T) | 0.02 | 0.29 (T) | 0.0001 | SLC1A3 |
| rs6682188 | 1 | 68,984,394 | T | −0.055 | 5.79E−06 | 0.65 (0) | 0.18 (T) | 0.0026 | 0.21 (T) | 0.0008 | DEPDC1-AS1 |
| rs17082453 | 4 | 54,011,603 | T | −0.109 | 5.84E−06 | 0.57 (0) | 0.07 (T) | 0.00072 | 0.03 (T) | 0.0027 | SCFD2 |
| rs7259473 | 19 | 39,493,010 | G | −0.045 | 7.31E−06 | 0.63 (0) | 0.49 (G) | 0.0026 | 0.33 (G) | 0.001 | FBXO17;FBXO27 |
| rs3851604 | 12 | 55,381,991 | G | −0.049 | 7.33E−06 | 0.30 (6.1) | 0.21 (A) | 0.00017 | 0.45 (A) | 0.01 | TESPA1;NEUROD4 |
| rs2477083 | 1 | 68,921,521 | G | −0.055 | 7.56E−06 | 0.55 (0) | 0.14 (G) | 0.00039 | 0.23 (G) | 0.006 | RPE65;DEPDC1 |
| rs4738003 | 8 | 70,542,552 | C | −0.045 | 7.77E−06 | 0.70 (0) | 0.48 (C) | 0.00038 | 0.31 (C) | 0.0077 | SULF1 |
| rs2555454 | 2 | 64,522,307 | A | −0.054 | 8.23E−06 | 0.12 (58.4) | 0.31 (A) | 0.0055 | 0.12 (A) | 0.00018 | LOC100507006; MIR4433B |
| rs7978952 | 12 | 55,397,643 | T | −0.047 | 9.44E−06 | 0.27 (18.9) | 0.22 (C) | 0.00015 | 0.39 (T) | 0.014 | TESPA1;NEUROD4 |
| Imputed SNPs (p < 5 × 10−8\) | |||||||||||
| rs1408065 | 6 | 133,192,978 | A | −0.071 | 4.49E−08 | 0.51(0) | 0.24(A) | 5.56E-07 | 0.08(A) | 0.04293 | RPS12;LINC00326 |
| rs7973023 | 12 | 55,357,264 | C | −0.059 | 1.95E−08 | 0.59(0) | 0.23(T) | 3.53E-05 | 0.47(C) | 0.000204 | TESPA1 |
| rs7973141 | 12 | 55,357,382 | C | −0.059 | 2.24E−08 | 0.65(0) | 0.23(T) | 5.03E-05 | 0.47(C) | 0.000171 | TESPA1 |
| rs7973347 | 12 | 55,357,387 | G | −0.059 | 2.24E−08 | 0.65(0) | 0.23(C) | 5.03E-05 | 0.47(G) | 0.000171 | TESPA1 |
| rs12301448 | 12 | 55,358,691 | T | −0.058 | 2.76E−08 | 0.60(0) | 0.23(C) | 4.91E-05 | 0.46(T) | 0.000207 | TESPA1 |
| rs1532052 | 12 | 55,361,314 | A | −0.058 | 2.03E−08 | 0.70(0) | 0.23(G) | 6.94E-05 | 0.46(A) | 0.000115 | TESPA1 |
| rs10783706 | 12 | 55,362,002 | G | −0.058 | 2.45E−08 | 0.81(0) | 0.23(A) | 0.000118 | 0.46(G) | 8.51E−05 | TESPA1 |
| rs10876674 | 12 | 55,362,156 | C | −0.057 | 4.60E−08 | 0.75(0) | 0.23(T) | 0.000118 | 0.46(C) | 0.000153 | TESPA1 |
| rs10876678 | 12 | 55,369,024 | A | −0.059 | 2.07E−08 | 0.98(0) | 0.24(G) | 0.000163 | 0.47(G) | 5.43E−05 | TESPA1 |
| rs1565170 | 12 | 55,369,858 | C | −0.061 | 7.29E−09 | 0.96(0) | 0.23(T) | 0.000118 | 0.44(T) | 2.72E−05 | TESPA1 |
| rs1565171 | 12 | 55,369,960 | C | −0.061 | 7.29E−09 | 0.96(0) | 0.23(A) | 0.000118 | 0.44(A) | 2.72E−05 | TESPA1 |
| rs1565172 | 12 | 55,370,164 | C | −0.061 | 7.29E−09 | 0.96(0) | 0.23(T) | 0.000118 | 0.44(T) | 2.72E−05 | TESPA1 |
| rs7314905 | 12 | 55,370,782 | G | −0.058 | 4.71E−08 | 0.80(0) | 0.23(C) | 0.000135 | 0.47(C) | 0.000141 | TESPA1 |
| rs7314940 | 12 | 55,370,948 | C | −0.059 | 3.39E−08 | 0.88(0) | 0.23(T) | 0.000135 | 0.42(T) | 0.000104 | TESPA1 |
| rs10876679 | 12 | 55,371,263 | C | −0.061 | 8.56E−09 | 0.96(0) | 0.23(A) | 0.000135 | 0.43(A) | 2.80E−05 | TESPA1 |
| rs7315419 | 12 | 55,371,307 | C | −0.061 | 8.53E−09 | 0.96(0) | 0.23(G) | 0.000135 | 0.43(G) | 2.78E−05 | TESPA1 |
| rs2046686 | 12 | 55,371,671 | C | −0.061 | 8.53E−09 | 0.96(0) | 0.23(T) | 0.000135 | 0.43(T) | 2.78E−05 | TESPA1 |
| rs11171205 | 12 | 55,372,239 | A | −0.058 | 4.71E−08 | 0.80(0) | 0.23(G) | 0.000135 | 0.47(G) | 0.000141 | TESPA1 |
| rs1488039 | 12 | 55,373,112 | G | −0.058 | 4.71E−08 | 0.80(0) | 0.23(A) | 0.000135 | 0.47(A) | 0.000141 | TESPA1 |
EA European Ancestry participants, AA Africa Ancestry participants, META GWAS meta-analysis, CHR chromosome, BP base pair (physical location) on genome (hg19), MAF minor allele frequency, P-value present refers to association test with EAA. I2 (P) heterogeneity index with P-value, TESPA1 Thymocyte Expressed, Positive Selection Associated 1, SLC1A3 solute carrier family 1 member 3, DEPDC1-AS1 DEP Domain Containing 1-Antisense RNA 1, TMPRSS15 Transmembrane Serine Protease 15, SULF1 Sulfatase 1, NPHP3 Nephrocystin 3, ACAD11 Acyl-CoA Dehydrogenase Family Member 11, SEC16B SEC16 Homolog B, Endoplasmic Reticulum Export Factor, SCFD2 Sec1 Family Domain Containing.
aEffect Allele corresponds to the effect size’s sign; it may not be the minor allele.