Table 3 SNPs nominally associated with schizophrenia (this study)

1

2

ZNF804A

rs7597593*

184668853

C

0.5

0.47

–

–

Riley et al.⁶⁰

2

2

ZNF804A

rs1344706

184913701

G

0.4

0.35

0.43

1.05 (0.92–1.20)

0.65

O’Donovan et al.⁵⁷

3

5

CTXN3-SLC12A2

rs245201*

127833520

G

0.5

0.44

–

–

Potkin et al.⁵⁸

4

6

BTN3A2

rs9393709**

26473126

T

0.3

0.35

0.64

0.97 (0.85–1.11)

0.54

Bamne et al.²³

5

6

Intergenic

rs926300

27167422

A

0.1

0.09

0.86

1.02 (0.82–1.27)

0.98

Shi et al.¹⁶

6

6

Intergenic

rs13219181

27244204

G

0.1

0.1

0.67

1.04 (0.85–1.29)

0.9

Glessner et al.¹²

7

6

Intergenic

rs13194053

27251862

C

0.1

0.1

0.95

0.99 (0.80–1.22)

0.98

Shi et al.¹⁶

8

6

Intergenic

rs3800307

27293771

A

0.1

0.14

0.31

0.90 (0.75–1.08)

0.46

Glessner et al.¹²

9

6

Intergenic

rs6932590

27356910

C

0.2

0.2

0.07

0.85 (0.73–1.00)

0.17

Stefansson et al.¹⁷

10

6

Intergenic

rs3800318

27371620

T

0.1

0.15

0.2

0.88 (0.74–1.06)

0.37

Glessner et al.¹²

11

6

HLA-N

rs3130375

30429711

A

0.02

0.01

0.33

1.30 (0.77–2.20)

NA

Int Consortium,¹⁵

12

6

HCP5

rs2244839

31546347

A

0.3

0.27

0.85

1.01 (0.88–1.17)

0.55

Shirts et al.²²

13

6

HCP5

rs14597

31547993

A

0.4

0.4

0.57

0.96 (0.85–1.09)

0.65

Unpublished work; dbSNP

14

6

HCP5

rs6940467

31550116

G

0.04

0.03

0.19

1.26 (0.89–1.76)

0.44

Unpublished work; dbSNP

15

6

HCP5

rs2523651

31556133

T

0.4

0.37

0.6

0.96 (0.85–1.10)

0.65

Shirts et al.²²

16

6

MICB

rs6916394**

31572029

C

0.4

0.4

0.96

1.0 (0.88–1.14)

0.02

Unpublished work; dbSNP

17

6

MICB

rs3828917

31573896

T

0.04

0.05

0.42

0.86 (0.64–1.15)

NA

Unpublished work; dbSNP

18

6

MICB

rs3130615^##

31583392

C

0.1

0.16

0.08

0.84 (0.71–1.01)

0.06

Stefansson et al.¹⁷

19

6

PPIAP9

rs2516489

31596017

A

0.3

0.3

0.58

0.96 (0.84–1.10)

0.86

Unpublished work; dbSNP

20

6

NFKBIL1

rs6916921

31628405

T

0.2

0.13

0.08

1.19 (1.00–1.43)

0.2

Unpublished work; dbSNP

21

6

NFKBIL1

rs2239707

31633298

G

0.3

0.31

0.59

0.96 (0.84–1.10)

0.85

Unpublished work; dbSNP

22

6

NFKBIL1

rs2230365

31633427

T

0.2

0.25

0.66

0.97 (0.84–1.12)

0.87

Unpublished work; dbSNP

23

6

LTA

rs1800610

31651806

T

0.1

0.13

0.33

1.11 (0.92–1.33)

0.56

Unpublished work; dbSNP

24

6

LST1

rs986475

31664688

C

0.2

0.13

0.13

1.17 (0.98–1.40)

0.32

Unpublished work; dbSNP

25

6

NOTCH4

rs2071278**

32273422

C

0.1

0.13

0.68

1.04 (0.86–1.25)

0.58

Stefansson et al.¹⁷

26

6

Intergenic

rs377763

32307122

T

0.3

0.27

0.58

1.04 (0.90–1.20)

0.67

Unpublished work; dbSNP

27

6

HLA-DQA1

rs9273012**

32719619

G

0.3

0.25

0.06

1.15 (1.0–1.32)

0.12

Glessner et al.¹²

28

6

AHI1

rs2064430

135684449

T

0.5

0.45

0.04

1.14 (1.0–1.30)

0.13

Doi et al.⁴³

29

6

Intergenic

rs1475069

136097927

C

0.4

0.41

0.42

1.05 (0.93–1.20)

0.66

Ingason et al.⁴⁷

30

7

RELN

rs7341475

103764368

A

0.1

0.12

0.67

0.18 (0.79–1.16)

0.63

Shifman et al.⁵⁹

31

11

NRGN

rs12807809

124736389

C

0.1

0.1

0.53

0.39 (0.76–1.15)

0.82

Stefansson et al.¹⁷

32

18

TCF4

rs9960767

55487771

C

0.2

0.22

0.36

0.85 (0.92–1.25)

0.51

Stefansson et al.¹⁷