Table 2 SNPs showing significance in stratified analysis among the three anatomical types of orofacial clefts: NSCLP, NSCLO and NSCPO in Chinese population.

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

Phenotype

Loci

SNP

BP (hg19)

Allele

F_A

F_U

P *

OR

NSCLP versus NSCLO

1q32.2

rs861020

209977111

A/G

0.23

0.30

2.05E−09

0.72 (0.65–0.80)

 

1q32.2

rs642961

209989270

A/G

0.23

0.30

1.16E−09

0.72 (0.64–0.80)

NSCLP versus NSCPO

1q32.2

rs861020

209977111

A/G

0.23

0.17

8.69E−11

1.51 (1.34–1.72)

 

1q32.2

rs642961

209989270

A/G

0.23

0.17

9.08E−11

1.51 (1.33–1.72)

 

1q32.2

rs2064163

210048819

A/C

0.38

0.44

6.41E−08

0.76 (0.69–0.84)

 

1q32.2

rs9430019

210050794

A/G

0.31

0.19

1.29E−25

1.87 (1.66–2.11)

 

2p25.1

rs287980

9971366

G/A

0.23

0.27

7.67E−04

0.83 (0.74–0.92)

 

2p25.1

rs287982

9972442

G/A

0.23

0.27

8.29E−04

0.83 (0.74–0.93)

 

2p24.2

rs10172734

16733054

G/A

0.26

0.33

6.31E−09

0.73 (0.66–0.81)

 

2p24.2

rs7552

16733928

A/G

0.24

0.28

6.33E−04

0.83 (0.74–0.92)

 

8q21.3

rs1034832

88918331

C/A

0.31

0.35

4.11E−04

0.83 (0.75–0.92)

 

12q21.1

rs2304269

72080272

G/A

0.39

0.45

8.58E−07

0.78 (0.71–0.86)

 

12q21.1

rs7967428

72089040

G/A

0.40

0.45

1.98E−06

0.79 (0.72–0.87)

 

16p13.3

rs2283487

3969886

G/A

0.42

0.47

3.21E−04

0.84 (0.76–0.92)

 

16p13.3

rs17136624

3996282

A/G

0.26

0.22

8.59E−04

1.22 (1.08–1.36)

 

17p13.1

rs2872615

8914693

G/A

0.43

0.49

2.59E−07

0.78 (0.70–0.85)

 

17p13.1

rs1880646

8929845

G/A

0.48

0.53

2.45E−04

0.83 (0.76–0.92)

 

17q21.32

rs1838105

45008935

A/G

0.44

0.38

2.28E−05

1.24 (1.12–1.37)

NSCLO versus NSCPO

1q32.2

rs861020

209977111

A/G

0.30

0.17

3.98E−24

2.10 (1.81–2.42)

 

1q32.2

rs642961

209989270

A/G

0.30

0.17

2.09E−24

2.11 (1.82–2.43)

 

1q32.2

rs2064163

210048819

A/C

0.39

0.44

1.21E−04

0.79 (0.70–0.89)

 

1q32.2

rs9430019

210050794

A/G

0.30

0.19

8.70E−18

1.84 (1.60–2.12)

 

2p24.2

rs10172734

16733054

G/A

0.25

0.33

6.20E−09

0.68 (0.59–0.77)

 

8q21.3

rs1034832

88918331

C/A

0.28

0.35

1.13E−06

0.73 (0.64–0.83)

 

10q25.3

rs6585429

118893231

G/A

0.38

0.43

1.11E−03

0.82 (0.72–0.92)

 

17p13.1

rs2872615

8914693

G/A

0.42

0.49

1.34E−05

0.77 (0.68–0.86)

  1. F_A, minor allele frequency in cases; F_U, minor allele frequency in controls; NSCLO, non-syndromic cleft lip only; NSCLP, non-syndromic cleft lip with palate; NSCPO, non-syndromic cleft palate only; OR, odds ratio; SNP, single-nucleotide polymorphism.
  2. OR is calculated based on minor allele; alleles are shown as minor allele/major allele.
  3. *P-value below 1.25 × 10−3 (0.05out of 40, the P-value using logistic regression test and Bonferroni correction) was considered to be statistically significant.
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