Table 2.
The common variants with statistically significant association with Parkinson’s disease in the meta-analysis of three cohorts
| Gene | Chr | Position | Ref allele | Mutant allele | SNP | D′ | R2 | CADD | Detailed annotation of the variant | Meta OR (95% CI) | Meta P-value |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MAPT | 17 | 44049329 | C | T | rs75242405 | 0.99 | 0.98 | NM_016835: intronic | 0.72 (0.64–0.81) | 1.05 × 10−7 | |
| MAPT | 17 | 44051846 | A | G | rs1800547 | 0.99 | 0.98 | NM_016835: intronic | 0.74 (0.62–0.89) | 1.24 × 10−3 | |
| MAPT | 17 | 44061023 | G | A | rs62063786 | 0.99 | 0.98 | 7.7 | NM_016835: exon6: c.G853A: p.D285N | 0.71 (0.63–0.79) | 2.42 × 10−9 |
| MAPT | 17 | 44061036 | T | C | rs62063787 | 0.99 | 0.98 | 0.001 | NM_016835: exon6: c.T866C: p.V289A | 0.71 (0.64–0.80) | 2.66 × 10−9 |
| MAPT | 17 | 44061278 | C | T | rs17651549 | 0.99 | 0.98 | 34 | NM_016835: exon6: c.C1108T: p.R370W | 0.71 (0.64–0.80) | 3.35 × 10−9 |
| MAPT | 17 | 44067400 | T | C | rs10445337 | 0.99 | 0.98 | 9.93 | NM_016835: exon8: c.T1339C: p.S447P | 0.74 (0.62–0.89) | 1.04 × 10−3 |
| MAPT | 17 | 44067508 | A | G | rs79447161 | 0.99 | 0.98 | NM_016835: intronic | 0.71 (0.64–0.80) | 6.01 × 10−9 | |
| MAPT | 17 | 44071294 | T | C | rs62063845 | 0.99 | 0.98 | NM_016835: intronic | 0.72 (0.64–0.80) | 6.82 × 10−9 | |
| MAPT | 17 | 44101563 | T | C | rs9468 | 0.99 | 0.98 | NM_016835: UTR3: c.*26T>C | 0.72 (0.64–0.81) | 8.35 × 10−9 | |
| MAPT | 17 | 44102604 | T | C | rs1052587 | 0.99 | 0.98 | NM_016835: UTR3: c.*1067T>C | 0.72 (0.65–0.81) | 9.98 × 10−9 | |
| MAPT | 17 | 44102638 | A | G | rs1052590 | 0.99 | 0.98 | NM_016835: UTR3: c.*1101A>G | 0.72 (0.64–0.81) | 9.51 × 10−9 | |
| MAPT | 17 | 44102865 | A | C | rs17574040 | 0.99 | 0.98 | NM_016835: UTR3: c.*1328A>C | 0.72 (0.64–0.80) | 4.79 × 10−9 | |
| MAPT a | 17 | 44103296 | T | C | rs7687 | 0.99 | 0.98 | NM_016835: UTR3: c.*1759T>C | 0.70 (0.62–0.78) | 8.28 × 10−10 | |
| MAPT | 17 | 44103616 | C | T | rs17652748 | 0.99 | 0.98 | NM_016835: UTR3: c.*2079C>T | 0.71 (0.64–0.80) | 3.81 × 10−9 | |
| MAPT | 17 | 44103825 | T | C | rs75010486 | 0.99 | 0.98 | NM_016835: UTR3: c.*2288T>C | 0.71 (0.64–0.80) | 4.02 × 10−9 | |
| MAPT | 17 | 44104343 | A | C | rs2158257 | 0.99 | 0.98 | NM_016835: UTR3: c.*2806A>C | 0.73 (0.65–0.81) | 2.36 × 10−8 | |
| MAPT | 17 | 44104410 | TCTC | T | rs568475466 | 0.99 | 0.98 | NM_016835: UTR3: c.*2874_*2876delCTC | 0.72 (0.64–0.80) | 7.73 × 10−9 | |
| TMEM175 | 4 | 944210 | A | C | rs34884217 | 1 | 0.01 | 0.2 | NM_032326: exon4: c.A194C: p.Q65P | 0.74 (0.63–0.87) | 2.11 × 10−4 |
| BST1 | 4 | 15717321 | G | A | rs3213710 | 0.94 | 0.79 | NM_004334: intronic | 1.22 (1.11–1.34) | 3.14 × 10−5 | |
| SNCA a | 4 | 90645671 | T | A | rs1045722 | 1 | 0.12 | NM_000345: UTR3: c.*2108A>T | 1.35 (1.17–1.56) | 4.08 × 10−5 | |
| SNCA | 4 | 90645674 | C | T | rs3857053 | 1 | 0.12 | NM_000345: UTR3: c.*2105G>A | 1.35 (1.17–1.56) | 4.56 × 10−5 | |
| GPNMB | 7 | 23300049 | A | C | rs199351 | 0.95 | 0.89 | NM_002510: intronic | 0.82 (0.75–0.90) | 2.70 × 10−5 | |
| GPNMB | 7 | 23307634 | ATGGG | A | rs2307783 | 0.95 | 0.89 | NM_002510: intronic | 0.83 (0.76–0.91) | 7.55 × 10−5 | |
| GPNMB a | 7 | 23314547 | C | T | rs5850 | 0.95 | 0.89 | NM_002510: UTR3: c.*704C>T | 0.81 (0.74–0.90) | 2.19 × 10−5 |
Chr = chromosome; CI = confidence interval; OR = odds ratio; Ref = reference; SNP = single nucleotide polymorphism.
a
Tagging SNP for the haplotype.