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Table 3 Top RF SNPs in the MS case-control dataset with LD pruning R2 = 0:99

From: An application of Random Forests to a genome-wide association dataset: Methodological considerations & new findings

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
  1. 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.