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Table 2 The top SNPs that CS-LMM identifies in an AD study with two known associations

From: Discovering weaker genetic associations guided by known associations

Rank

SNP

Chr

Chr Position

Est. Coe.

MAF

Gene

Disease [Literature]

1

rs2075650

19

44892362

0.21

0.18

APOE

AD [38]

2

rs157580

19

44892009

0.02

0.27

TOMM40

AD [39]

3

rs10027926

4

3412927

-8.3E-11

0.14

RGS12

SCZ [40]

4

rs12641989

4

3418113

-7.8E-11

0.14

RGS12

SCZ [40]

5

rs3088231

4

3420484

-7.5E-11

0.13

RGS12

SCZ [40]

6

rs10512523

17

69044919

5.2E-11

0.28

ABCA9

AD [41]

7

rs4076949

1

234066399

4.2E-11

0.18

SLC35F3

 

8

rs874418

4

3440342

-3.9E-11

0.19

HGFAC

 

9

rs6842419

4

3475572

-3.2E-11

0.16

DOK7

 

10

rs16844383

4

3445516

-2.9E-11

0.21

HGFAC

 

11

rs12131508

1

234017193

1.7E-11

0.17

SLC35F3

 

12

rs12506821

4

3282833

-1.6E-11

0.16

  

13

rs11485175

1

222437868

1.4E-11

0.23

  

14

rs584507

10

6489788

1.2E-11

0.24

PRKCQ

 

15

rs12563692

1

216818264

-1.2E-11

0.30

ESRRG

ALC [42, 43]

16

rs6446731

4

3283024

-1.1E-11

0.26

  

17

rs7984051

13

70233817

-8.1E-12

0.25

  

18

rs2327771

20

13295734

3.0E-12

0.29

ISM1

 

19

rs7548651

1

234012812

2.4E-12

0.20

SLC35F3

 

20

rs4330674

8

133209259

-1.2E-12

0.24

WISP1

 

21

rs16885750

5

56578982

-8.1E-13

0.12

C5orf67

 

22

rs938412

3

188571269

3.6E-13

0.31

LPP

 
  1. The SNPs are ranked by the absolute values of their estimated coefficients. The first two SNPs with largest coefficients are known SNPs the model takes as a prior knowledge. The rest are SNPs predicted by the model. The MAFs reported in the table are calculated using the AD GWAS data. The information of whether a SNP is located within a region of a gene is taken from the dbSNP. Abbreviations: ALC, Alchoholism; AD, Alzheimer’s Disease; SCZ, Schizophrenia; Est. Coe.: Estimated Coefficients. Note that the literature support may refer to how the genes that the corresponding SNPs reside in are related to the phenotype, instead of the SNPs themselves. See discussions in Section Alzheimer’s Disease Study for details.