Table 2.
Summary of genetic variants examined
| Variant | Nearby gene | Chr. | Position | Type of variant | MA | MAF from the current study | MAF in a normal Caucasian populationc | OR (p-value) from Nalls et al. study [4]d |
|---|---|---|---|---|---|---|---|---|
| rs10788972a | TCEANC2 | 1 | 54572243 | Intronic | A | 47.5% | 44.0% | 0.64 (6.2 × 10−8) |
| rs35749011 | GBA/SYT11 | 1 | 155135036 | Intergenic | A | 2.7% | 2.2% | 1.82 (1.4 × 10−29) |
| rs114138760b | GBA/SYT11 | 1 | 154925709 | Intronic | C | 1.8% | 1.2% | 1.57 (3.8 × 10−7) |
| rs823118 | RAB7L1/NUCKS1 | 1 | 205723572 | Intergenic | C | 44.8% | 46.5% | 0.89 (1.7 × 10−16) |
| rs10797576 | SIPA1L2 | 1 | 232664611 | Intronic | T | 13.9% | 13.8% | 1.13 (4.9 × 10−10) |
| rs6430538 | ACMSD/TMEM163 | 2 | 135539967 | Intergenic | T | 43.4% | 49.7% | 0.88 (9.1 × 10−20) |
| rs1955337 | STK39 | 2 | 168272635 | Intergenic | A | 12.5% | 11.8% | 1.21 (1.2 × 10−20) |
| rs12637471 | MCCC1 | 3 | 182762437 | Intronic | A | 20.3% | 19.8% | 0.84 (2.1 × 10−21) |
| rs34311866 | TMEM175/GAK/DGKQ | 4 | 951947 | Missense | C | 24.4% | 18.7% | 1.27 (1.0 × 10−43) |
| rs34884217b | TMEM175/GAK/DGKQ | 4 | 950422 | Missense | G | 8.4% | 9.6% | 0.80 (1.1 × 10−6) |
| rs11724635 | BST1 | 4 | 15737101 | Intronic | C | 43.3% | 44.0% | 0.89 (9.4 × 10−18) |
| rs6812193 | FAM47E/SCARB2 | 4 | 77198986 | Intronic | T | 37.6% | 39.0% | 0.91 (3.0 × 10−11) |
| rs356182 | SNCA | 4 | 90626111 | Intergenic | G | 35.4% | 36.2% | 1.32 (4.2 × 10−73) |
| rs3910105b | SNCA | 4 | 89761420 | Intronic | C | 49.1% | 44.3% | 0.84 (7.1 × 10−19) |
| rs9275326 | HLA-DQB1 | 6 | 32666660 | Intergenic | T | 8.5% | 10.4% | 0.83 (1.2 × 10−12) |
| rs13201101b | HLA-DQB1 | 6 | 32375827 | Intergenic | T | 5.2% | 6.9% | 1.19 (3.8 × 10−6) |
| rs199347 | GPNMB | 7 | 23293746 | Intronic | C | 38.5% | 38.3% | 0.90 (1.2 × 10−12) |
| rs591323 | FGF20 | 8 | 16697091 | Intergenic | T | 25.6% | 28.9% | 0.92 (6.7 × 10−8) |
| rs117896735 | INPP5F | 10 | 119776815 | Intronic | A | 1.2% | 1.3% | 1.62 (4.4 × 10−13) |
| rs329648 | MIR4697 | 11 | 133765367 | Intergenic | T | 35.5% | 33.3% | 1.11 (9.8 × 10−12) |
| rs76904798 | LRRK2 | 12 | 40614434 | Intergenic | T | 13.5% | 12.7% | 1.16 (5.2 × 10−14) |
| rs11060180 | CCDC62 | 12 | 123303586 | Intronic | G | 48.0% | 43.5% | 0.90 (6.0 × 10−12) |
| rs11158026 | GCH1 | 14 | 55348869 | Intronic | T | 32.7% | 31.1% | 0.90 (5.9 × 10−11) |
| rs2414739 | VPS13C | 15 | 61994134 | Intergenic | G | 28.3% | 27.9% | 0.90 (1.3 × 10−11) |
| rs14235 | BCKDK/STX1B | 16 | 31121793 | Synonymous | A | 41.5% | 38.2% | 1.10 (2.4 × 10−12) |
| rs11868035 | SREBF/RAI1 | 17 | 17715101 | Intergenic | A | 31.6% | 33.8% | 0.94 (6.0 × 10−5) |
| rs17649553 | MAPT | 17 | 43994648 | Intronic | A | 22.8% | 24.1% | 0.77 (2.4 × 10−48) |
| rs12456492 | RIT2 | 18 | 40673380 | Intronic | G | 30.9% | 33.8% | 1.11 (7.7 × 10−12) |
| rs55785911 | DDRGK1 | 20 | 3168166 | Intergenic | A | 37.2% | 38.7% | 1.11 (3.0 × 10−11) |
MA=minor allele; MAF=minor allele frequency; OR=odds ratio.
rs10788972 was included not due to a significant association in the Nalls et al. GWAS meta-analysis [4], but rather due to an association observed by the GWAS performed by Beecham et al. [18] which utilized neuropathologically confirmed PD patients and controls.
Indicates a variant included due to a significant association with risk of Parkinson’s disease risk that was independent of the other variant in the given gene that had the strongest association signal.
MAF in a normal Caucasian population was obtained using 1000 Genomes Project Phase 3 data.
To be consistent with the results of our study, the OR from the Nalls et al. study that we provide is that associated with the minor allele of the given variant in our study.