Table 3.
CCT-associated variants from the conditional and joint analysis of the meta-analysis of European studies and replication in Asians
| SNP | Chr:bp | Nearest gene | Annotation | Previously reported SNP (ref)a | A1/A2 | Meta-analysis in Europeans | CoJo analysis in Europeans | Meta-analysis in Asians | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A1F | β (SE) | P | A1F | β (SE) | P COJO | LD_r | A1F | β (SE) | P | ||||||
| rs1309531 | 5:64306311 | CWC27 | Intronic | a/t | 0.55 | −2.4 (0.379) | 2.439E-10 | 0.56 | −2.096 (0.383) | 4.28E-08 | 0.130 | 0.63 | −1.184 (0.547) | 3.03E-02 | |
| rs10064391 | 5:64686659 | ADAMTS6 | Intronic | rs230712117 | a/g | 0.63 | −2.765 (0.397) | 3.182E-12 | 0.62 | −2.484 (0.4) | 5.53E-10 | 0.000 | 0.70 | −0.889 (0.601) | 1.39E-01 |
| rs1931656 | 6:82610188 | 148 kb 5’ of FAM46A | Intronic | a/t | 0.45 | 2.172 (0.391) | 2.749E-08 | 0.45 | 2.383 (0.393) | 1.31E-09 | −0.104 | 0.47 | 2.965 (0.529) | 2.13E-08 | |
| rs9361886 | 6:82778502 | 101 kb 3’ of IBTK | Intergenic | rs153813817 | t/c | 0.54 | 2.391 (0.445) | 7.665E-08 | 0.56 | 2.637 (0.447) | 3.66E-09 | 0.000 | 0.57 | 2.35 (0.66) | 3.67E-04 |
| rs3094339 | 9:136884738 | VAV2-BRD3 | Intergenic | a/g | 0.71 | −2.804 (0.426) | 4.682E-11 | 0.72 | −3.042 (0.427) | 1.01E-12 | −0.008 | 0.53 | 0.671 (0.559) | 2.30E-01 | |
| rs4841899 | 9:137424412 | 92 kb 3’ of RXRA | Intergenic | rs4842044, rs153647866,67 | t/c | 0.67 | −2.993 (0.405) | 1.413E-13 | 0.67 | −2.289 (0.416) | 3.60E-08 | −0.037 | 0.63 | −2.383 (0.596) | 6.32E-05 |
| rs1536482 | 9:137440528 | 93 kb 5’ of COL5A1 | Intergenic | rs3132306, rs3118516, rs311852017,68 | g/a | 0.66 | 4.569 (0.399) | 1.95E-30 | 0.66 | 3.455 (0.425) | 4.60E-16 | 0.388 | 0.68 | 2.864 (0.601) | 1.85E-06 |
| rs3132303 | 9:137444298 | 89 kb 5’ of COL5A1 | Intergenic | c/g | 0.26 | 5.236 (0.497) | 6.11E-26 | 0.26 | 3.55 (0.544) | 6.86E-11 | −0.039 | 0.26 | 5.912 (0.714) | 1.21E-16 | |
| rs7032489 | 9:137559775 | COL5A1 | Intronic | rs704452917 | c/g | 0.86 | 4.033 (0.547) | 1.637E-13 | 0.86 | 4.296 (0.548) | 4.64E-15 | −0.008 | 0.81 | 1.845 (0.685) | 7.08E-03 |
| rs116878472 | 12:104210992 | NT5DC3 | Intronic | t/c | 0.97 | −8.392 (1.506) | 2.523E-08 | 0.97 | −8.829 (1.509) | 4.95E-09 | −0.058 | NA | NA | NA | |
| rs11111869 | 12:104402485 | GLT8D2 | Intronic | rs156489217 | g/a | 0.83 | −3.174 (0.51) | 4.77E-10 | 0.83 | −3.308 (0.511) | 9.40E-11 | 0.000 | 0.78 | −3.479 (0.636) | 4.38E-08 |
| rs2034809 | 15:101555399 | LRRK1 | Intronic | rs4965359 | g/a | 0.51 | 1.844 (0.4) | 4.047E-06 | 0.51 | 2.545 (0.407) | 3.82E-10 | −0.177 | 0.34 | 2.161 (0.579) | 1.88E-04 |
| rs930847 | 15:101558562 | LRRK1 | Intronic | rs93084717 | g/t | 0.23 | 3.573 (0.453) | 3.194E-15 | 0.22 | 3.955 (0.461) | 9.17E-18 | −0.042 | 0.27 | 3.793 (0.617) | 7.82E-10 |
| rs752092 | 15:101781934 | CHSY1 | Intronic | a/g | 0.66 | −2.205 (0.396) | 2.554E-08 | 0.67 | −2.19 (0.397) | 3.46E-08 | 0.000 | 0.79 | −1.745 (0.652) | 7.40E-03 | |
| rs35193497 | 16:88324821 | 169 kb 5’ of ZNF469 | Intergenic | rs654022317 | t/g | 0.36 | −6.238 (0.434) | 8.637E-47 | 0.34 | −4.654 (0.495) | 4.90E-21 | 0.653 | 0.29 | −4.928 (0.622) | 2.34E-15 |
| rs28687756 | 16:88328928 | 165 kb 5’ of ZNF469 | Intergenic | t/g | 0.57 | −7.507 (0.584) | 8.418E-38 | 0.53 | −4.566 (0.667) | 7.84E-12 | 0.000 | NA | NA | NA | |
Results from the conditional and joint analysis, genotype data from BMES cohort was used (N = 2582)
Nearest gene, (reference NCBI build37) is given as locus label, but this should not be interpreted as providing support that the nearest gene is the best candidate, a list including all the genes +/− 200 kb of the lead SNP is presented in Supplementary Table 12
SNP rsID, Chr:bp chromosome: base pair, A1 risk allele, A2 other allele, A1F frequency of allele A1, β effect size on CCT based on allele A1, SE standard error of the effect size, i insertion, d deletion, r reference, PCOJO = P-value after CoJo analyses
aSNPs in LD (r2 > 0.5) with SNP from CoJo analyses. In bold novel independent CCT-associated SNPs