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Table 2 Top SNPs identified by Random Forests in MS case-control dataset without 6p data

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
12 rs1805755 M6PR < 0.01 1 73.42 1.05 * 10-17
7 rs6467970 SEMA3A* (44.1 kb) 0.19 2 19.71 9.00 * 10-6
10 rs10823051 CTNNA3 0.16 3 17.61 2.71 * 10-5
1 rs10754012 RGS1* (3.3 mb) 0.23 4 22.24 2.41 * 10-5
12 rs1716167 MPHOSPH9 0.21 5 22.38 2.23 * 10-6
6 rs1015340 PHACTR2 0.47 6 14.86 1.16 * 10-4
10 rs7068990 PPAPDC1A* (137.6 kb) 0.23 7 17.65 2.65 * 10-5
8 rs1466526 FAM164A* (86.0 kb) 0.25 8 15.60 7.84 * 10-5
6 rs1040638 PHACTR2 0.48 9 13.82 2.01 * 10-4
7 rs16217 NPY* (292.9 kb) 0.26 10 7.14 7.53 * 10-3
12 rs1106240 PITPNM2 0.20 11 18.71 1.52 * 10-5
8 rs4739135 FAM164A* (98.8 kb) 0.19 12 16.33 5.34 * 10-5
18 rs4798684 ADCYAP1* (19.8 kb) 0.30 13 13.41 2.51 * 10-4
6 rs1015341 PHACTR2 0.47 14 14.88 1.14 * 10-4
12 rs2695478 MPHOSPH9 0.20 15 17.30 3.19 * 10-5
1 rs11800848 EVI5 0.26 16 19.04 1.28 * 10-5
9 rs6993386 IL7 0.32 17 17.95 2.27 * 10-5
6 rs6915752 PHACTR2 0.45 18 17.71 2.57 * 10-5
20 rs2223712 BTBD3* (3.6 kb) 0.19 19 11.86 5.73 * 10-4
10 rs7092549 PPAPDC1A* (140.0 kb) 0.23 20 17.06 3.62 * 10-5
6 rs9376783 PHACTR2 0.45 21 17.26 3.27 * 10-5
17 rs17652139 CCL2* (3.0 mb) 0.23 22 11.81 5.88 * 10-4
7 rs740295 MGC87402 0.31 23 7.89 4.96 * 10-3
5 rs156823 ARL15 0.47 24 12.13 4.97 * 10-4
18 rs7241142 ADCYAP1* (20.7 kb) 0.30 25 10.81 1.01 * 10-3
  1. The top 25 SNPs from RF analysis of the dataset without chromosome 6 SNPs are shown above. The minor allele frequency (MAF) is derived from controls and the χ2-statistic is from univariate testing. *Indicates that the gene is the closest gene with distance.