Table 2 Allele and genotype frequency of single SNP association analysis.

From: Evaluation of association of common variants in HTR1A and HTR5A with schizophrenia and executive function

Dataset

Gene

SNP Affection

H-WE

OR2 95% CI

Allelic count (Freq. %)

Allelic P-value1

Genotype count (Freq. %)

Genotypic P-value1

The discovery dataset

HTR1A

rs878567

  

G

A

 

GG

GA

AA

 
  

SCZ

0.113

1.24

1843(82.65)

387(17.35)

0.001541

754(67.62)

335(30.04)

26(2.33)

0.001584

  

CTR

0.453

1.08–1.41

3635(79.4)

943(20.6)

0.04623

1449(63.3)

737(32.2)

103(4.5)

0.04752

  

rs6295

  

C

G

 

CC

CG

GG

 
  

SCZ

0.159

1.15

1711(76.73)

519(23.27)

0.018648

648(58.12)

415(37.22)

52(4.66)

0.024294

  

CTR

0.634

1.02–1.30

3392(74.09)

1186(25.91)

0.55944

1261(55.09)

870(38.01)

158(6.9)

0.72882

 

HTR5A

rs1800883

  

C

G

 

CC

CG

GG

 
  

SCZ

0.339

1.21

1083(48.57)

1147(51.43)

0.000264

255(22.87)

573(51.39)

287(25.74)

0.000899

  

CTR

0.847

1.09–1.34

2439(53.28)

2139(46.72)

0.00792

652(28.48)

1135(49.58)

502(21.93)

0.02697

  

rs6320

  

T

A

 

TT

TA

AA

 
  

SCZ

0.755

1.14

1453(65.16)

777(34.84)

0.017216

471(42.24)

511(45.83)

133(11.93)

0.055259

  

CTR

0.807

1.02–1.26

2847(62.19)

1731(37.81)

0.51648

888(38.79)

1071(46.79)

330(14.42)

 

The replication dataset

HTR1A

rs878567

  

G

A

 

GG

GA

AA

 
  

SCZ

0.479

1.19

3508(82.42)

748(17.58)

0.000508

1441(67.72)

626(29.42)

61(2.87)

0.002009

  

CTR

0.969

1.08–1.31

6169(79.81)

1561(20.19)

0.00508

2462(63.7)

1245(32.21)

158(4.09)

0.02009

  

rs6295

  

C

G

 

CC

CG

GG

 
  

SCZ

0.366

1.09

3243(76.2)

1013(23.8)

0.068321

1228(57.71)

787(36.98)

113(5.31)

0.106148

  

CTR

0.522

0.98–1.18

5774(74.7)

1956(25.3)

 

2164(55.99)

1446(37.41)

255(6.6)

 
 

HTR5A

rs1800883

  

C

G

 

CC

CG

GG

 
  

SCZ

0.463

1.13

2111(49.6)

2145(50.4)

0.001095

532(25)

1047(49.2)

549(25.8)

0.003746

  

CTR

0.841

1.05–1.22

4075(52.72)

3655(47.28)

0.01095

1071(27.71)

1933(50.01)

861(22.28)

0.03746

  

rs6320

  

T

A

 

TT

TA

AA

 
  

SCZ

0.684

1.08

2759(64.83)

1497(35.17)

0.058870

890(41.82)

979(46.01)

259(12.17)

0.151378

  

CTR

0.809

0.99–1.17

4877(63.09)

2853(36.91)

 

1542(39.9)

1793(46.39)

530(13.71)

 
  1. SCZ: schizophrenia; CTR: control; CI: confidence interval; OR: odds ratio.
  2. 1Risk allele and significant P values are in bold italics, and corrected P values are underlined after the Bonferroni correction (P × 30 in the discovery stage and P × 10 in the replication stage). A P-value of 0.05 was chosen as the threshold for significance.
  3. 2OR refers to the risk allele odds ratio in cases and controls.
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