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Table 3 Meta-analysis of SIREN and COMPASS studies for fixed effects (FE), conventional random effects (RE), alternate random effects (RE2), and binary effects (BE) models from METASOFT

From: Novel functional insights into ischemic stroke biology provided by the first genome-wide association study of stroke in indigenous Africans

Chr.

rsID

Position Hg38

Gene region hg38

Gene(s) hg38

Ref/Alt

P-value RE2

P-value BE

I2

SIREN P-value

COMPASS P-value

Effect size dir*

2

rs142655108

4036068

Intergenic

LOC105373394-LINC01249

C/A

7.16E−07

2.70E−07

80.22

4.63E−01

9.64E−08

+ +

3

rs6440776

151678293

Intergenic

MIR5186-AADACL2

C/T

8.05E−06

6.48E−07

94.82

1.95E−07

8.74E−01

− -

 

rs184221467

153407501

Ncrna intronic

LINC02006

G/A

5.51E−08

1.44E−07

0

1.92E−02

7.79E−07

+ +

5

rs116123543

169439420

Intergenic

SLIT3-SPDL1

C/T

1.21E−06

2.96E−06

0

3.87E−02

8.04E−06

+ +

 

rs268515

9478268

Intronic

SEMA5A

C/T

6.70E−07

1.49E−06

0

6.39E−02

2.60E−06

+ +

7

rs2194650

53526642

Intergenic

POM121L12-LINC01446

T/C

4.57E−06

8.63E−07

93.37

2.53E−07

2.92E−01

+ +

 

rs184901586

66707028

Intronic

RABGEF1

A/C

1.21E−06

2.63E−06

0

2.63E−01

1.89E−06

− -

8

rs112455974

1624708

Intronic

DLGAP2

C/A

1.59E−06

9.26E−07

65.99

4.51E−01

3.79E−07

+ +

 

rs11995798

77080739

Intergenic

PEX2-LOC102724874

G/C

9.40E−07

2.51E−06

0

1.27E−03

1.06E−04

+ +

9

rs12348429

136761594

Intronic

LCN15

G/A

3.19E−07

8.87E−07

0

6.45E−03

1.21E−05

+ +

 

rs565295967

69860276

Intronic

C9orf135

C/T

1.81E−06

7.43E−07

71.41

9.65E−01

2.41E−07

− +

10

rs184882114

133387813

Intronic

PAOX

C/T

8.82E−07

1.74E−05

96.27

8.23E−04

5.00E−06

− +

 

rs150576982

22779332

Intergenic

PIP4K2A-ARMC3

G/C

3.71E−07

9.87E−07

0

2.41E−02

4.22E−06

+ +

 

rs74469072

51787504

Intronic

PRKG1

G/T

7.49E−07

6.62E−07

52.72

3.17E−01

3.46E−07

+ +

 

rs145597261

5543158

Intergenic

OLFM5P-OR52H1

T/C

3.45E−07

9.75E−07

0

4.89E−03

1.74E−05

− -

 

rs7107345

5556565

Intergenic

OR52H1-OR52B6

A/C

2.38E−07

6.51E−07

0

3.03E−03

1.69E−05

− -

12

rs192977447

119104946

Intronic

SRRM4

T/A

1.70E−06

5.86E−07

93.21

1.23E−01

1.77E−07

− +

 

rs55931441

120977406

Intergenic

HNF1A-AS1-HNF1A

G/A

2.82E−07

1.20E−07

70.68

5.99E−01

4.58E−08

+ +

14

rs10498430

51476243

ncRNA intronic

FRMD6-AS2

C/T

5.85E−07

1.60E−06

0

4.90E−03

2.85E−05

+ +

16

rs114318459

81767653

Intergenic

CMIP-PLCG2

T/C

1.12E−06

2.65E−06

0

4.50E−02

6.31E−06

− -

19

rs12982680

34661176

ncRNA intronic

SCGB1B2P

G/A

8.43E−07

2.25E−06

0

1.51E−02

1.50E−05

+ +

 

rs187158875

39518254

Intronic

SELENOV

G/A

7.03E−07

1.46E−06

0

4.74E−02

2.97E−06

+ +

22

rs116127899

47568929

Intergenic

LINC01644-LINC00898

G/A

7.15E−07

1.51E−06

0

1.67E−01

1.46E−06

+ +

  1. *Effect size direction order: SIREN, COMPASS; We used the baseline model from SIREN for meta-analysis: Stroke Status ~ Sex + Age + PCs1…10 + SNP