Table 3. Loci identified in age at onset analysis.
Suggestive variants identified in the discovery stage (p<10−5) and followed-up in the replication stage, as well as the meta-analyses are represented. Variant p-values and beta values were calculated using an additive genetic model. Minor alleles were treated as effect alleles. The locus name is determined by the closest gene to the significant variant. MAF=minor allele frequency; P=p-value.
| Discovery | Replication | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Positiona | Major/ minor allele |
Locus name |
MAF patients/controls |
Association | MAF patients/controls |
Association | Meta-analysisb | ||||
| Beta (95%CI) |
P | Beta (95%CI) |
P | Beta (95%CI) |
P | I2 | ||||||
| rs116316277 | 2:185834886 | C/T | ZNF804A | 0·03 | 8·09(4·72 − 11·6) | 3·58×10−6 | 0·08 | −1·03(-6·79 − 4·72) | 7·26 × 10−1 | 5·76(2·85 − 8·67) | 1·04×10−4 | 86·1 |
| rs6809184 | 3:170888198 | C/T | TNIK | 0·05 | −6·78(−9·24 – −4·32) | 1·22×10−7 | 0·09 | −0·54(−5·29 − 4·21) | 8·24 × 10−1 | −5·46(−7·64 – −3·27) | 1·01×10−6 | 80·9 |
| rs12189587 | 6:165332257 | C/T | C6orf11 | 0·11 | −4·05(−5·76 – −2·34) | 4·83×10−6 | 0·13 | 1·4(−2·32 − 5·11) | 4·62 × 10−1 | −3·1(−4·65 – −1·54) | 9·44×10−5 | 85·3 |
| rs6962939 | 7:7524226 | T/A | COL28A1 | 0·04 | −6·02(−8·61 – −3·43) | 7·00×10−6 | 0·06 | −6·15(−12·56 − 0·25) | 6·13 × 10−2 | −6·04(−8·43 – −3·64) | 8·18×10−7 | 0 |
| rs2922921 | 7:96398079 | G/A | SHFM1 | 0·02 | 9·65(5·58 − 13·72) | 4·65×10−6 | 0·06 | −0·54(−7·77 − 6·7) | 8·84 × 10−1 | 7·20(3·65 − 10·75) | 6·93×10−5 | 82·7 |
| rs77466830 | 7:151529171 | C/A | PRKAG2 | 0·32 | 2·91(1·64 − 4·18) | 9·49×10−6 | 0·43 | −0·13(−2·36 − 2·11) | 9·12 × 10−1 | 2·17(1·06 − 3·27) | 1·18×10−4 | 81·3 |
| rs9792144 | 8:53081551 | C/G | ST18 | 0·12 | 3·99(2·30 − 5·68) | 4·88×10−6 | 0·18 | 2·99(−0·26 − 6·24) | 7·28 × 10−2 | 3·78(2·28 − 5·28) | 7·55×10−7 | 0 |
| rs3922636 | 8:80383502 | G/A | STMN2 | 0·19 | 3·28(1·89 − 4·67) | 5·08×10−6 | 0·31 | 0·49(−2·23 − 3·21) | 7·23 × 10−1 | 2·70(1·47 − 3·94) | 1·83×10−5 | 68·4 |
| rs12943707 | 17:73317510 | C/G | GRB2 | 0·29 | −2·8(−4·00 – −1·6) | 6·40×10−6 | 0·4 | −0·41(−2·80 − 1·98) | 7·38 × 10−1 | −2·32(−3·39 – −1·25) | 2·22×10−5 | 67·5 |
| rs1561819 | 18:2712629 | G/A | SMCHD1 | 0·49 | −2·41(−3·46 – −1·36) | 8·96×10−6 | 0·51 | −0·81(−2·97 − 1·35) | 4·61 × 10−1 | −2·11(−3·05 – −1·16) | 1·23×10−5 | 41·5 |
| rs6108746 | 20:10902771 | T/C | JAG1 | 0·19 | 3·54(2·19 − 4·89) | 4·23×10−7 | 0·25 | 1·69(−1·11 − 4·48) | 2·38 × 10−1 | 3·19(1·98 − 4·41) | 2·59×10−7 | 27·4 |
| rs6111609 | 20:17664546 | C/A | RRBP1 | 0·22 | 2·86(1·61 − 4·11) | 9·83×10−6 | 0·22 | 2·88(−0·03 − 5·8) | 5·41 × 10−2 | 2·86(1·71 − 4·01) | 1·05×10−6 | 0 |
a
Positions are based on the Human Genome version 38 (hg38).
b
For SNPs with I2 >0.3, a random effects meta-analysis was also performed. The p-values were generally larger in the random effects meta-analysis, and the results were consistent with the fixed effects, showing that none of these SNPs were significantly associated with the outcome.