Table 1

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

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


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.

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

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