Table 1.
Results of discovery and replication association analyses.
| SNP Information | Discovery phase (13,728 cases and 95,282 controls) | Replication phase (5,353 cases and 5,551 controls) | Joint phase (19,081 cases and 100,833 controls) | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| ||||||||||||
| SNP | C | Position (bp) | Nearest gene(s) | Effect allele | Alternate allele | Effect allele frequency | Odds ratio | P | Odds ratio | P | Odds ratio | P |
| Genome Wide Significant, Discovery Phase | ||||||||||||
|
| ||||||||||||
| rs35749011* | 1 | 155,135,036 | GBA/SYT11 | a | g | 0.017 | 1.762 | 6.09×10-23 | 2.307 | 7.48×10-09 | 1.824 | 1.37×-29 |
| rs823118 | 1 | 205,723,572 | RAB7L1/NUCKS1 | t | c | 0.559 | 1.126 | 1.36×10-13 | 1.109 | 1.43×10-04 | 1.122 | 1.66×-16 |
| rs10797576 | 1 | 232,664,611 | SIPA1L2 | t | c | 0.14 | 1.139 | 1.19×10-08 | 1.11 | 3.38×10-03 | 1.131 | 4.87×-10 |
| rs6430538 | 2 | 135,539,967 | ACMSD/TMEM163 | t | c | 0.43 | 0.873 | 5.56×10-15 | 0.882 | 9.42×10-06 | 0.875 | 9.13×-20 |
| rs1474055* | 2 | 169,110,394 | STK39 | t | c | 0.128 | 1.213 | 7.12×10-16 | 1.218 | 1.07×10-06 | 1.214 | 1.15×-20 |
| rs115185635* | 3 | 87,520,857 | KRT8P25/APOOP2 | c | g | 0.035 | 1.789 | 2.18×10-08 | 0.931 | 0.846 | 1.142 | 0.022 |
| rs12637471 | 3 | 182,762,437 | MCCC1 | a | g | 0.193 | 0.844 | 3.32×10-16 | 0.836 | 3.72×10-07 | 0.842 | 2.14×-21 |
| rs34311866 | 4 | 951,947 | TMEM175/GAK/DGKQ | t | c | 0.809 | 0.784 | 3.58×10-33 | 0.791 | 6.29×10-12 | 0.786 | 1.02×-43 |
| rs11724635 | 4 | 15,737,101 | BST1 | a | c | 0.553 | 1.122 | 8.07×10-13 | 1.138 | 2.73×10-06 | 1.126 | 9.44×-18 |
| rs6812193 | 4 | 77,198,986 | FAM47E/SCARB2 | t | c | 0.364 | 0.897 | 7.17×10-11 | 0.935 | 0.011 | 0.907 | 2.95×-11 |
| rs356182 | 4 | 90,626,111 | SNCA | a | g | 0.633 | 0.737 | 3.23×10-67 | 0.822 | 1.75×10-12 | 0.760 | 4.16×-73 |
| rs9275326* | 6 | 32,666,660 | HLA-DQB1 | t | c | 0.094 | 0.797 | 5.82×10-13 | 0.9 | 0.018 | 0.826 | 1.19×-12 |
| rs199347 | 7 | 23,293,746 | GPNMB | a | g | 0.59 | 1.123 | 2.37×10-12 | 1.072 | 7.66×10-03 | 1.110 | 1.18×-12 |
| rs117896735* | 10 | 121,536,327 | INPP5F | a | g | 0.014 | 1.767 | 1.21×10-11 | 1.404 | 1.10×10-03 | 1.624 | 4.34×-13 |
| rs3793947* | 11 | 83,544,472 | DLG2 | a | g | 0.443 | 0.912 | 2.59×10-08 | 0.976 | 0.201 | 0.929 | 3.96×-07 |
| rs329648 | 11 | 133,765,367 | MIR4697 | t | c | 0.354 | 1.1 | 1.65×10-08 | 1.121 | 4.38×10-05 | 1.105 | 9.83×-12 |
| rs76904798 | 12 | 40,614,434 | LRRK2 | t | c | 0.143 | 1.17 | 1.33×10-12 | 1.11 | 3.69×10-03 | 1.155 | 5.24×-14 |
| rs11060180 | 12 | 123,303,586 | CCDC62 | a | g | 0.558 | 1.101 | 2.14×10-08 | 1.114 | 7.26×10-05 | 1.105 | 6.02×-12 |
| rs11158026 | 14 | 55,348,869 | GCH1 | t | c | 0.335 | 0.889 | 7.13×10-11 | 0.948 | 0.039 | 0.904 | 5.85×-11 |
| rs1555399* | 14 | 67,984,370 | TMEM229B | a | t | 0.468 | 0.872 | 5.53×10-16 | 0.971 | 0.144 | 0.897 | 6.63×-14 |
| rs2414739 | 15 | 61,994,134 | VPS13C | a | g | 0.734 | 1.114 | 4.13×10-09 | 1.109 | 7.96×10-04 | 1.113 | 1.23×-11 |
| rs14235 | 16 | 31,121,793 | BCKDK/STX1B | a | g | 0.381 | 1.094 | 3.89×10-08 | 1.133 | 7.72×10-06 | 1.103 | 2.43×-12 |
| rs17649553 | 17 | 43,994,648 | MAPT | t | c | 0.226 | 0.771 | 4.86×10-37 | 0.764 | 7.03×10-15 | 0.769 | 2.37×-48 |
| rs12456492 | 18 | 40,673,380 | RIT2 | a | g | 0.693 | 0.905 | 5.12×10-09 | 0.9 | 2.16×10-04 | 0.904 | 7.74×-12 |
| rs62120679* | 19 | 2,363,319 | SPPL2B | t | c | 0.314 | 1.141 | 2.53×10-09 | 0.999 | 0.518 | 1.097 | 5.57×-07 |
| rs8118008* | 20 | 3,168,166 | DDRGK1 | a | g | 0.657 | 1.111 | 2.32×10-08 | 1.113 | 1.18×10-04 | 1.111 | 3.04×-11 |
|
| ||||||||||||
| Previously Reported as Significant in Genome Wide Studies | ||||||||||||
|
| ||||||||||||
| rs34016896 | 3 | 160,992,864 | NMD3 | t | c | 0.319 | 1.08 | 7.68×10-06 | 1.028 | 0.174 | 1.067 | 1.08×-05 |
| rs591323 | 8 | 16,697,091 | FGF20 | a | g | 0.275 | 0.921 | 1.30×10-05 | 0.902 | 6.16×10-04 | 0.916 | 6.68×-08 |
| rs60298754 | 8 | 89,373,041 | MMP16 | t | c | 0.024 | 1.078 | 0.181 | - | - | 1.078 | 0.181 |
| rs7077361 | 10 | 15,561,543 | ITGA8 | t | c | 0.874 | 1.11 | 3.24×10-05 | 1.044 | 0.154 | 1.092 | 4.16×-05 |
| rs11868035 | 17 | 17,715,101 | SREBF/RAI1 | a | g | 0.298 | 0.937 | 2.17×10-04 | 0.947 | 0.036 | 0.939 | 5.98×-05 |
| rs2823357 | 21 | 16,914,905 | USP25 | a | g | 0.37 | 1.036 | 0.032 | 1.018 | 0.267 | 1.031 | 0.027 |
C - Chromosome; OR - odds ratio
*
replication genotyping for these SNPs failed assay design or quality control and a suitable proxy variant was selected (rs35749011, proxy rs71628662; rs1474055, proxy rs1955337; rs115185635, proxy rs62267708; rs117896735, proxy rs118117788; rs3793947, proxy rs12283611; rs1555399, proxy rs1077989; rs62120679, proxy rs10402629; rs8118008, proxy rs55785911). Note, only replication phase p-values are one-sided. Nearest gene or previously published proximal gene names included in table.