Table 3 |
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|
Top RF SNPs in the MS case-control dataset with LD pruning R2 = 0:99 |
||||||
|
Chr |
SNP |
Gene |
MAF |
RF Rank |
CHISQ |
P-Value |
|
|
||||||
|
7 |
rs6467970 |
SEMA3A* (44.1 kb) |
0.19 |
1 |
19.71 |
9.00 * 10-6 |
|
|
||||||
|
8 |
rs1466526 |
FAM164A* (86.0 kb) |
0.25 |
2 |
15.60 |
7.84 * 10-5 |
|
|
||||||
|
12 |
rs1716167 |
MPHOSPH9 |
0.21 |
3 |
22.38 |
2.23 * 10-6 |
|
|
||||||
|
10 |
rs10823051 |
CTNNA3 |
0.16 |
4 |
17.61 |
2.71 * 10-5 |
|
|
||||||
|
1 |
rs11800848 |
EVI5 |
0.26 |
5 |
19.04 |
1.28 * 10-5 |
|
|
||||||
|
17 |
rs17652139 |
CCL2* (3.0 mb) |
0.23 |
6 |
11.81 |
5.88 * 10-4 |
|
|
||||||
|
6 |
rs1015341 |
PHACTR2 |
0.47 |
7 |
14.88 |
1.14 * 10-4 |
|
|
||||||
|
7 |
rs16217 |
NPY* (292.9 kb) |
0.26 |
8 |
7.14 |
7.53 * 10-3 |
|
|
||||||
|
1 |
rs12743520 |
EVI5 |
0.26 |
9 |
18.61 |
1.61 * 10-5 |
|
|
||||||
|
6 |
rs1040638 |
PHACTR2 |
0.48 |
10 |
13.82 |
2.01 * 10-4 |
|
|
||||||
|
18 |
rs4798684 |
ADYCAP1* (19.8 kb) |
0.30 |
11 |
13.41 |
2.51 * 10-4 |
|
|
||||||
|
8 |
rs6993386 |
IL7 |
0.32 |
12 |
17.95 |
2.27 * 10-5 |
|
|
||||||
|
1 |
rs2760524 |
RGS1* (3.3 mb) |
0.19 |
13 |
20.00 |
7.76 * 10-6 |
|
|
||||||
|
10 |
rs7092549 |
PPAPDC1A* (140.0 kb) |
0.23 |
14 |
17.06 |
3.62 * 10-5 |
|
|
||||||
|
20 |
rs2223712 |
BTBD3* (3.6 kb) |
0.19 |
15 |
11.86 |
5.72 * 10-5 |
|
|
||||||
|
7 |
rs740295 |
MGC87402 |
0.31 |
16 |
7.90 |
4.96 * 10-5 |
|
|
||||||
|
1 |
rs282177 |
RPS6KA1 |
0.26 |
17 |
17.01 |
3.72 * 10-5 |
|
|
||||||
|
6 |
rs6570578 |
PHACTR2 |
0.45 |
18 |
17.00 |
3.72 * 10-5 |
|
|
||||||
|
10 |
rs7068990 |
PPAPDC1A* (137.6 kb) |
0.23 |
19 |
17.65 |
2.65 * 10-5 |
|
|
||||||
|
1 |
rs1359062 |
RGS1* (3.3 mb) |
0.19 |
20 |
18.49 |
1.71 * 10-5 |
|
|
||||||
|
2 |
rs698853 |
LOC100302652 |
0.28 |
21 |
16.75 |
4.26 * 10-5 |
|
|
||||||
|
7 |
rs156293 |
NPY* (313.8 kb) |
0.22 |
22 |
9.56 |
1.99 * 10-5 |
|
|
||||||
|
16 |
rs6499946 |
KLKBL4 |
0.22 |
23 |
12.83 |
3.41 * 10-4 |
|
|
||||||
|
2 |
rs7583622 |
ASB3 |
0.23 |
24 |
17.07 |
3.60 * 10-5 |
|
|
||||||
|
20 |
rs17408919 |
PAK7 |
0.23 |
25 |
11.63 |
6.50 * 10-4 |
|
|
||||||
|
The top 25 SNPs from RF analysis of the dataset without chromosome 6 SNPs are shown above in the R2 = 0:99 runs after 3 sub-samplings. Results are similar to analysis of full dataset. *Indicates that the gene is the closest gene with distance. |
||||||
|
Goldstein et al. BMC Genetics 2010 11:49 doi:10.1186/1471-2156-11-49 |
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