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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.