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Table 1 Top SNPs identified by Random Forests in MS case-control dataset

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
6 rs3129900 C6orf10 0.17 1 272.2 3.75 * 10-61
6 rs3129934 C6orf10 0.17 2 274.4 1.28 * 10-61
6 rs9270986 HLA Tag SNP 0.17 3 274.6 1.14 * 10-61
6 rs3129768 HLA-DQA* (70 bp) 0.20 4 238.9 3.14 * 10-53
6 rs2647046 HLA-DQA2* (8.5 kb) 0.39 5 113.9 1.38 * 10-26
6 rs3129932 C6orf10 0.23 6 219.8 1.02 * 10-49
6 rs9275572 HLA-DQA2* (2.1 kb) 0.42 7 101.5 7.24 * 10-24
6 rs3131294 NOTCH4 0.14 8 215.4 9.26 * 10-49
6 rs910049 C6orf10 0.24 9 222.2 2.98 * 10-50
6 rs2894249 C6orf10 0.23 10 220.7 6.28 * 10-50
6 rs3135377 HLA-DRA* (80.6 kb) 0.21 11 217.9 2.60 * 10-49
6 rs9469220 HLA-DQA2* (18.5 kb) 0.50 12 99.2 2.28 * 10-23
6 rs7194 HLA-DRA 0.40 13 129.7 4.69 * 10-30
6 rs6457620 HLA-DQB1* (137.5 kb) 0.49 14 96.03 1.13 * 10-22
6 rs3130287 TNXB 0.15 15 181.2 2.72 * 10-41
6 rs6457617 HLA-DQB1 (137.4 kb) 0.49 16 96.03 1.13 * 10-22
6 rs6936204 C6orf10* (14.6 kb) 0.36 17 113.3 1.83 * 10-26
12 rs1805755 M6PR ¡ .01 18 73.42 1.05 * 10-17
12 rs1716167 MPHOSPH9 0.21 19 22.38 2.23 * 10-6
7 rs17708673 C7orf25 (106.2 kb) 0.16 20 6.357 1.17 * 10-2
6 rs9268877 HLA-DRA* (126.3 kb) 0.42 21 74.57 5.85 * 10-18
6 rs9276440 HLA-DQA2 0.45 22 83.75 5.63 * 10-20
6 rs2621383 HLA-DOB* (825.5 kb) 0.37 23 82.72 9.44 * 10-20
22 rs80515 FAM19A5* (1.4 mb) 0.10 24 3.751 5.28 * 10-2
20 rs2425754 CDH22* (580.3 kb) 0.15 25 4.193 4.06 * 10-2
  1. The top 25 SNPs from RF analysis of the whole dataset are shown above. Most of the top SNPs are on chromosome 6p within the HLA region. 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.