Table 4

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

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


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.

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

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