Table 1 Association results for markers from the 14 novel NSCLP risk loci at each stage.

From: Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity

loci

SNP

BP (hg19)

Alleles *

NSCLP GWAS (above) and NSCLP replication (below)

NSCLP Meta

NSCLO replication (above) and NSCPO replication (below)

NSCL/P replication 1

NSCL/P replication 2 (above) and NSCL/P replication 3 (below)

1000 Genomes

    

F_A

F_U

P

OR

P (F)

OR(F)

F_A

F_U

P

OR

F_A

F_U

P

OR

MAF

P

RR

MAF_CHB

MAF_EUR

2p25.1

rs287980

9971366

G/A

0.23

0.27

1.99E−05

0.82

1.94E−08

0.83

0.25

0.26

2.34E−01

0.93

0.20

0.21

5.34E−01

0.94

0.26

4.63E−01

0.94

0.28

0.22

    

0.23

0.27

5.54E−04

0.84

  

0.27

0.26

7.87E−01

1.02

    

0.21

7.62E−01

0.97

  

2p25.1

rs287982

9972442

G/A

0.23

0.27

1.58E−05

0.82

6.15E−09

0.82

0.25

0.26

1.65E−01

0.92

0.20

0.21

5.21E−01

0.94

0.26

4.63E−01

0.94

0.28

0.22

    

0.23

0.27

2.28E−04

0.83

  

0.27

0.26

7.63E−01

1.02

    

0.21

6.85E−01

0.96

  

4p16.2

rs34246903

4794195

C/A

0.38

0.43

2.57E−05

0.82

4.45E−08

0.85

0.40

0.42

2.91E−01

0.95

0.30

0.34

2.39E−02

0.82

0.42

2.54E−02

0.85

0.41

0.33

    

0.40

0.43

1.09E−02

0.89

  

0.41

0.42

7.77E−01

0.99

    

0.33

1.65E−01

1.13

  

4p16.2

rs1907989

4818925

A/G

0.46

0.51

2.29E−06

0.81

1.58E−08

0.85

0.48

0.50

6.42E−02

0.91

0.57

0.61

1.92E−02

0.83

0.49

3.91E−03

1.22

0.52

0.64

    

0.48

0.50

1.94E−02

0.90

  

0.50

0.50

5.78E−01

1.03

    

0.36

5.14E−01

1.06

  

4q28.1

rs908822

124906257

A/G

0.10

0.07

6.13E−07

1.46

4.33E−08

1.31

0.09

0.08

7.64E−02

1.17

0.08

0.07

2.44E−01

1.20

0.08

7.14E−03

1.41

0.07

0.06

    

0.10

0.09

4.46E−02

1.16

  

0.09

0.08

5.21E−01

1.06

    

0.07

3.80E−01

1.15

  

5p12

rs10462065

44068846

A/C

0.24

0.20

3.51E−07

1.26

1.12E−08

1.22

0.24

0.22

7.92E−02

1.11

0.11

0.11

7.28E−01

0.96

0.24

3.01E−02

1.19

0.19

0.10

    

0.23

0.20

2.04E−03

1.18

  

0.22

0.22

7.17E−01

0.98

    

0.12

6.66E–01

1.05

  

6p24.3

rs9381107

9469238

A/G

0.31

0.37

1.97E−09

0.79

2.72E−09

0.83

0.32

0.35

4.79E−02

0.90

0.16

0.18

1.43E−01

0.85

0.32

8.43E−01

1.02

0.33

0.16

    

0.33

0.36

1.40E−02

0.89

  

0.34

0.35

2.81E−01

0.95

    

0.15

7.75E−01

0.97

  

8p11.23

rs13317

38269514

G/A

0.30

0.34

4.10E−06

0.83

3.96E−08

0.85

0.31

0.33

7.59E−02

0.91

0.21

0.22

4.46E−01

0.93

0.31

2.65E−01

0.92

0.39

0.25

    

0.32

0.35

7.43E−03

0.88

  

0.32

0.33

3.83E−01

0.95

    

0.23

3.17E−03

0.76

  

8q22.1

rs12681366

95401265

G/A

0.44

0.49

2.95E−06

0.82

2.35E−10

0.83

0.46

0.48

6.16E−02

0.91

0.32

0.34

3.01E−01

0.92

0.45

5.62E−01

0.96

0.48

0.35

    

0.44

0.48

2.48E−04

0.85

  

0.47

0.48

4.01E−01

0.96

    

0.31

2.28E−01

0.90

  

8q22.1

rs957448

95541302

G/A

0.44

0.50

3.78E−10

0.78

9.60E−13

0.81

0.47

0.49

5.72E−02

0.91

0.23

0.26

1.49E−01

0.87

0.47

1.18E−01

0.90

0.51

0.31

    

0.46

0.49

7.59E−04

0.86

  

0.48

0.49

1.33E−01

0.93

    

0.23

4.07E−01

0.92

  

9q22.32

rs10512248

98259703

C/A

0.29

0.34

1.80E−07

0.79

5.10E−10

0.82

0.33

0.35

4.47E−02

0.90

0.34

0.33

4.34E−01

1.07

0.28

1.41E−02

0.81

0.31

0.32

    

0.30

0.33

3.19E−03

0.87

  

0.31

0.35

1.23E−04

0.82

    

0.32

1.00E−01

0.86

  

12q13.13

rs3741442

53346750

G/A

0.46

0.41

1.17E−06

1.22

3.72E−12

1.22

0.44

0.42

6.42E−02

1.10

0.99

1.00

5.42E−01

0.72

0.54

1.30E−04

0.77

0.41

0.98

    

0.46

0.41

3.36E−06

1.23

  

0.44

0.42

9.72E−02

1.09

    

0.02

2.52E−02

0.48

  

12q13.2

rs705704

56435412

A/G

0.27

0.23

4.39E−05

1.22

1.29E−09

1.22

0.24

0.25

2.84E−01

0.94

0.34

0.31

7.44E−02

1.16

0.23

6.61E−01

1.04

0.24

0.33

    

0.28

0.24

5.97E−05

1.22

  

0.25

0.25

1.00E+00

1.00

    

0.35

1.15E−03

1.32

  

12q21.1

rs2304269

72080272

G/A

0.38

0.44

1.07E−07

0.79

1.32E−12

0.81

0.41

0.44

2.04E−02

0.89

0.05

0.05

7.81E−01

0.95

0.43

2.66E−02

0.85

0.55

0.06

    

0.41

0.45

1.12E−04

0.84

  

0.45

0.44

3.03E−01

1.05

    

0.07

6.17E−01

0.92

  

12q21.1

rs7967428

72089040

G/A

0.38

0.44

1.63E−07

0.79

3.08E−12

0.81

0.41

0.44

6.56E−02

0.91

0.05

0.05

9.91E−01

1.00

0.43

2.32E−02

0.85

0.55

0.06

    

0.41

0.45

1.57E−04

0.84

  

0.45

0.44

1.72E−01

1.07

    

0.07

6.78E−01

0.93

  

14q22.1

rs7148069

51839645

A/G

0.23

0.19

1.94E−05

1.27

1.69E−08

1.22

0.21

0.20

6.21E−01

1.03

0.32

0.33

7.92E−01

0.98

0.17

8.75E−01

1.02

0.19

0.33

    

0.22

0.20

7.21E−03

1.16

  

0.19

0.20

4.90E−01

0.96

    

0.31

3.06E−01

1.11

  

14q32.13

rs1243572

95379499

G/A

0.48

0.42

1.37E−07

1.26

3.52E−10

1.20

0.47

0.43

7.75E−04

1.18

0.79

0.78

3.65E−01

1.09

0.57

7.84E−01

0.98

0.40

0.79

    

0.45

0.42

6.09E−03

1.13

  

0.44

0.43

2.14E−01

1.06

    

0.23

4.99E−01

0.94

  

14q32.13

rs1243573

95379583

C/A

0.48

0.42

2.83E−07

1.25

8.61E−10

1.20

0.46

0.43

8.19E−03

1.14

0.80

0.78

4.10E−01

1.09

0.57

7.84E−01

0.98

0.40

0.79

    

0.45

0.42

7.30E−03

1.13

  

0.45

0.43

8.60E−02

1.09

    

0.23

4.99E−01

0.94

  

17q21.32

rs4968247

44988703

A/G

0.37

0.41

4.11E−06

0.84

8.70E−10

0.83

0.37

0.40

1.44E−03

0.85

0.66

0.67

4.81E−01

0.94

0.61

2.52E−03

1.26

0.43

0.65

    

0.37

0.41

2.43E−05

0.83

  

0.40

0.40

4.34E−01

0.96

    

0.33

1.21E−01

1.15

  

17q21.32

rs1838105

45008935

A/G

0.45

0.39

1.84E−07

1.26

1.31E−11

1.22

0.43

0.38

5.98E−04

1.19

0.39

0.33

5.83E−03

1.27

0.40

1.43E−02

1.19

0.38

0.37

    

0.42

0.38

3.48E−04

1.17

  

0.38

0.38

9.30E−01

1.00

    

0.38

1.37E−01

1.13

  
  1. F_A, allele frequency in cases; F_U, allele frequency in controls; GWAS. Genome-wide association study; NSCLO, non-syndromic cleft lip only; NSCLP, non-syndromic cleft lip with palate; NSCPO, non-syndromic cleft palate only; SNP, single-nucleotide polymorphism.
  2. NSCLP GWAS: study in 2,033 NSCLP cases and 4,051 controls of Chinese Han (the P-value using logistic regression test); NSCLP replication: replication study in 1,346 NSCLP cases and 4,542 controls of Chinese Han (the P-value using logistic regression test); NSCLP Meta: Meta analysis of NSCLP GWAS and NSCLP replication using fixed model (the P-value using Cochran–Mantel–Haenszel test); NSCLO replication: replication study in 1,104 NSCLO cases and 3,312 controls of Chinese Han (the P-value using logistic regression test); NSCPO replication: replication study in 1,104 NSCPO cases and 3,312 controls shared with NSCLO replication of Chinese Han (the P-value using logistic regression test); NSCL/P replication 1: replication study in 399 NSCL/P cases and 1,318 controls of Central Europeans (the P-value using logistic regression test); NSCL/P replication 2: replication study in 861 NSCL/P case-parent trios of Asian ancestry (the P-value using logistic regression test); NSCL/P replication 3: replication study in 557 NSCL/P case–parent trios of European American ancestry (the P-value using logistic regression test).
  3. *Alleles: shown as minor allele/major allele in Chinese Han samples. Bold denotes entries that reached the thresholds of significance.
Back to article page