Table 2.
A: SNP Association to onset age under linkage peaks on Chromosomes 1.
| SNP | ref allele | chr | BP position | cM position | gene symbol | Control MAF | LRRK2 MAF | All effect estimate | All p-value | G2019S only effect estimate | G2019S only p-value |
|---|---|---|---|---|---|---|---|---|---|---|---|
| rs2186024 | C | 1 | 190,696,708 | 190.66 | RGS1 | 0.45 | 0.43 | -4.60 | 0.00068 | -3.13 | 0.03575 |
| rs2494354 | G | 1 | 192,721,321 | 193.26 | 0.10 | 0.06 | -8.31 | 0.0047 | -6.30 | 0.0759 | |
| rs2494312 | C | 1 | 192,763,213 | 193.28 | 0.11 | 0.07 | -7.85 | 0.0043 | -6.40 | 0.0521 | |
| rs927724 | C | 1 | 194,441,413 | 193.87 | KCNT2 | 0.12 | 0.11 | 7.13 | 0.0030 | 7.06 | 0.0059 |
| rs599779 | A | 1 | 197,604,771 | 195.46 | 0.40 | 0.39 | 4.52 | 0.0023 | 4.16 | 0.0109 | |
| rs1898240 | G | 1 | 197,613,703 | 195.47 | 0.20 | 0.15 | 5.85 | 0.0046 | 5.24 | 0.0148 | |
| rs487359 | A | 1 | 197,648,234 | 195.49 | 0.37 | 0.31 | 4.58 | 0.0015 | 4.65 | 0.0032 | |
| rs1890133 | T | 1 | 197,721,501 | 195.54 | 0.24 | 0.23 | -4.40 | 0.0048 | -2.49 | 0.1374 | |
| rs10919967 | T | 1 | 198,769,294 | 196.41 | 0.19 | 0.15 | 1.82 | 0.4443 | 7.93 | 0.0022 | |
| rs1400875 | G | 1 | 200,088,066 | 199.67 | IPO9 | 0.32 | 0.29 | -4.40 | 0.0043 | -2.65 | 0.1394 |
| rs2820312 | T | 1 | 200,135,880 | 199.86 | LMOD1 | 0.32 | 0.29 | -4.40 | 0.0043 | -2.65 | 0.1394 |
| rs3087949 | C | 1 | 201,314,244 | 202.52 | PPFIA4 | 0.29 | 0.32 | -2.99 | 0.0395 | -4.57 | 0.0024 |
| rs2050935 | C | 1 | 201,598,170 | 203.24 | FMOD | 0.20 | 0.18 | -5.80 | 0.0037 | -5.13 | 0.0244 |
| rs4950978 | T | 1 | 203,291,196 | 205.91 | CNTN2 | 0.23 | 0.23 | -4.63 | 0.0028 | -3.74 | 0.0211 |
| rs1470637 | T | 1 | 203,299,906 | 205.92 | CNTN2 | 0.34 | 0.36 | -3.73 | 0.0045 | -2.85 | 0.0367 |
| B: SNP Association to onset age under linkage peaks on Chromosomes 16. | |||||||||||
| rs7200879 | G | 16 | 30,855,073 | 56.80 | FBXL19 | 0.23 | 0.23 | 3.44 | 0.04620 | 5.29 | 0.00485 |
| rs1344528 | G | 16 | 48,099,429 | 59.05 | ZNF423 | 0.45 | 0.43 | -3.69 | 0.0080 | -4.58 | 0.0025 |
| rs7204293 | A | 16 | 48,585,606 | 59.77 | TMEM188 | 0.08 | 0.09 | -8.27 | 0.0025 | -7.28 | 0.0188 |
| rs1861662 | T | 16 | 48,664,884 | 59.84 | HEATR3 | 0.08 | 0.08 | -7.52 | 0.0045 | -6.55 | 0.0319 |
| rs4785239 | T | 16 | 49,758,032 | 61.67 | SALL1 | 0.15 | 0.14 | 6.57 | 0.0013 | 6.70 | 0.0034 |
| rs11645369 | C | 16 | 51,507,565 | 65.31 | 0.25 | 0.20 | -6.12 | 0.0017 | -5.12 | 0.0216 | |
| rs3095635 | G | 16 | 52,098,599 | 66.77 | AKTIP | 0.18 | 0.10 | -6.69 | 0.0031 | -6.52 | 0.0128 |
| rs1075440 | C | 16 | 52,348,407 | 67.17 | FTO | 0.32 | 0.24 | -4.53 | 0.0017 | -3.03 | 0.0848 |
| rs17224310 | A | 16 | 52,548,454 | 67.49 | FTO | 0.17 | 0.20 | 4.52 | 0.0107 | 5.22 | 0.0043 |
| rs7206456 | A | 16 | 52,562,990 | 67.51 | FTO | 0.29 | 0.33 | -3.77 | 0.0048 | -3.96 | 0.0047 |
| rs4784384 | T | 16 | 53,029,562 | 68.25 | 0.32 | 0.35 | 4.34 | 0.0022 | 4.51 | 0.0033 | |
| rs893265 | G | 16 | 53,864,590 | 70.30 | IRX6 | 0.37 | 0.38 | -3.72 | 0.0025 | -4.11 | 0.0026 |
| rs2397442 | T | 16 | 53,866,761 | 70.31 | IRX6 | 0.50 | 0.44 | 4.43 | 0.0004 | 4.06 | 0.0038 |
| rs30935 | C | 16 | 53,878,002 | 70.37 | IRX6 | 0.43 | 0.42 | 5.11 | 0.0001 | 4.67 | 0.0010 |
| rs733140 | C | 16 | 53,881,595 | 70.39 | IRX6 | 0.23 | 0.20 | -3.73 | 0.0105 | -4.63 | 0.0028 |
| rs11860394 | G | 16 | 53,884,305 | 70.40 | IRX6 | 0.35 | 0.35 | -3.87 | 0.0037 | -3.04 | 0.0420 |
| rs10521323 | A | 16 | 54,038,722 | 70.70 | MMP2 | 0.25 | 0.28 | 4.58 | 0.0005 | 4.15 | 0.0033 |
| rs1420228 | C | 16 | 54,042,674 | 70.70 | MMP2 | 0.11 | 0.18 | -5.83 | 0.0022 | -5.23 | 0.0109 |
| rs243842 | C | 16 | 54,084,923 | 70.70 | MMP2 | 0.39 | 0.37 | 4.52 | 0.0010 | 4.34 | 0.0029 |
| rs899228 | G | 16 | 54,944,789 | 71.69 | GNAO1 | 0.22 | 0.20 | 4.84 | 0.0041 | 4.69 | 0.0078 |
a
Nearest genes within 100kb of SNP