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Table 1 The top SNPs that CS-LMM identifies in an alcoholism study with four known associations

From: Discovering weaker genetic associations guided by known associations

Rank

SNP

Chr

Chr Position

Est. Coe.

MAF

Gene

Disease [Literature]

1

rs1789891

4

99329262

4.2E3

0.15

ADH1B

ALC [27]

2

rs7590720

2

216033935

1.7E3

0.29

PECR

ALC [28]; AD [29]

3

rs2835872

21

37654970

1.5E3

0.25

KCNJ6

ALC [30]; DS [31]

4

rs4478858

1

31411078

1.4E3

0.44

SERINC2

ALC [32]

5

rs1789924

4

99353129

-2.2E-4

0.33

ADH1C

ALC [33]

6

rs698

4

99339632

-2.2E-4

0.33

ADH1C

ALC [33]

7

rs2851300

4

99358667

-2.2E-4

0.33

  

8

rs10483038

21

37652469

-1.6E-4

0.25

KCNJ6

ALC [30]; DS [31]

9

rs1344694

2

216028914

-1.3E-4

0.32

PECR

ALC [28]; AD [29]

10

rs4147536

4

99317955

-7.6E-5

0.30

ADH1B

ALC [27]

11

rs12482570

21

37705475

-5.9E-5

0.28

KCNJ6

ALC [30]; DS [31]

12

rs857975

21

37629311

-5.8E-5

0.28

KCNJ6

ALC [30]; DS [31]

13

rs4147544

4

99213357

-5.7E-5

0.45

ADH6

ALC [34]

14

rs702860

21

37636327

-5.6E-5

0.26

KCNJ6

ALC [30]; DS [31]

15

rs2835853

21

37642590

-5.6E-5

0.26

KCNJ6

ALC [30]; DS [31]

16

rs717859

21

37640500

-5.6E-5

0.26

KCNJ6

ALC [30]; DS [31]

17

rs11499823

4

99353592

-5.6E-5

0.12

ADH1C

ALC [33]

18

rs2835910

21

37713604

-5.5E-5

0.30

KCNJ6

ALC [30]; DS [31]

19

rs4355398

4

99237168

-3.8E-5

0.25

  

20

rs2187483

4

99212946

-9.7E-7

0.38

ADH6

ALC [34]

21

rs2835831

21

37614931

-6.9E-7

0.30

  
  1. The SNPs are ranked by the absolute values of their estimated coefficients. The first four SNPs with the largest coefficients in the upper panel are known SNPs that our model CS-LMM takes as prior knowledge. The rest SNPs in the lower panel are ones predicted by the model. The MAFs reported in the table are calculated using the case-control alcoholism GWAS data. The information of whether a SNP is located within a region of a gene is taken from the Database for Single Nucleotide Polymorphisms (dbSNP) [35], and listed in the ’Gene’ column. Abbreviations: ALC, Alcoholism; AD, Alzheimer’s Disease; DS, Down Syndrome; 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 Alcoholism Study for details