Skip to main content

Table 4 Top RF SNPs in the MS case-control dataset with LD pruning R2 = 0.90

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
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 * 10-6
6 rs1040638 PHACTR2 0.48 5 13.82 2.01 * 10-4
8 rs4739135 FAM164A* (98.8 kb) 0.19 6 16.33 5.34 * 10-5
18 rs4798684 ADCYAP1* (19.8 kb) 0.30 7 13.41 2.51 * 10-4
10 rs7092549 PPAPDC1A* (140.0 kb) 0.23 8 17.06 3.62 * 10-5
14 rs10483442 NPAS3 0.19 9 13.88 1.95 * 10-4
20 rs2223712 BTBD3* (3.6 kb) 0.19 10 11.86 2.71 * 10-4
12 rs1106240 PITPNM2 0.20 11 18.71 1.52 * 10-5
5 rs156823 ARL15 0.47 12 12.13 4.97 * 10-4
9 rs10975130 KANK1 0.16 13 24.04 7.81 * 10-6
12 rs12578774 AACS* (1.3 mb) 0.31 14 19.67 9.19 * 10-6
2 rs7583622 ASB3 0.23 15 17.07 3.60 * 10-5
6 rs6570578 PHACTR2 0.45 16 17.00 3.73 * 10-5
1 rs282177 RPS6KA1 0.26 17 17.01 3.72 * 10-5
5 rs11949767 MXD3* (59.7 kb) 0.26 18 17.79 2.47 * 10-5
10 rs7427 MSRB2 0.36 19 10.64 1.10 * 10-3
8 rs1879818 TRAPPC9 0.30 20 7.35 6.72 * 10-3
16 rs1974876 CCDC113 0.15 21 10.91 9.55 * 10-3
17 rs11651517 GAS7 0.43 22 10.29 1.34 * 10-3
20 rs6018946 BLCAP* (581.3 kb) 0.34 23 16.85 4.04 * 10-5
2 rs11694785 ARHGAP25 0.40 24 10.15 1.44 * 10-3
2 rs6746541 ATOH8 0.35 25 16.06 6.14 * 10-5
  1. The top 25 SNPs from RF analysis of the dataset without chromosome 6 SNPs are shown above in the R2 = 0.90 runs after 3 sub-samplings. Results are similar to the analysis of full dataset, though there is more heterogenetity in the top findings, owing primarily to LD pruning. *Indicates that the gene is the closest gene with distance.