Table 3

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

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


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.

Goldstein et al. BMC Genetics 2010 11:49   doi:10.1186/1471-2156-11-49

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