Skip to main content

Table 4 Effect sizes of SNPs with the lowest p-values from the analysis of ALSPAC children

From: Association of SNPs in LCP1 and CTIF with hearing in 11 year old children: Findings from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort and the G-EAR consortium

10 most significant SNPs associated with high frequency hearing overall (max n = 4970)

SNP

Chromosome

Base Position

Gene

Effect Size (dB)

p-value

LD Block

Minor allele

MAF

rs12959910

18

46337861

CTIF

0.61

0.00079

19

G

0.11

rs8085434

18

46200968

CTIF

0.84

0.0024

8

C

0.05

rs8091955

18

46358907

CTIF

0.34

0.0036

22

G

0.45

rs1994559

18

46332358

CTIF

0.43

0.0043

19

A

0.17

rs1319946

18

46359024

CTIF

0.31

0.0067

22

C

0.49

rs1877192

2

167863420

XIRP2

0.43

0.014

3

C

0.12

rs10825335

10

56234349

PCDH15

0.41

0.022

18

A

0.11

rs1317625

18

46380182

CTIF

0.3

0.026

25

A

0.22

rs7233521

18

46219733

CTIF

0.43

0.031

11

A

0.09

rs1316826

18

46348156

CTIF

0.26

0.032

18

C

0.31

10 most significant SNPs associated with high frequency hearing in males (max n = 2445)

SNP

Chromosome

Base Position

Gene

Effect Size (dB)

p-value

LD Block

Minor allele

MAF

rs2337069

18

46120940

CTIF

0.58

0.0041

3

T

0.22

rs16951446

18

47599093

MYO5B

−1.06

0.0047

8

G

0.05

rs16951488

18

47610821

MYO5B

−1.06

0.0047

8

G

0.05

rs8085434

18

46200968

CTIF

1.04

0.0093

8

C

0.05

rs10823837

10

73498910

CDH23

0.44

0.0094

1

C

0.43

rs1877192

2

167863420

XIRP2

0.65

0.011

3

C

0.12

rs11662494

18

46241017

CTIF

−0.57

0.012

13

T

0.15

rs10825335

10

56234349

PCDH15

0.67

0.012

18

A

0.11

rs869000

2

167862974

XIRP2

0.74

0.019

3

C

0.07

rs4939612

18

47541612

MYO5B

0.52

0.022

7

T

0.16

10 most significant SNPs associated with high frequency hearing in females (max n = 2525)

SNP

Chromosome

Base Position

Gene

Effect Size (dB)

p-value

LD Block

Minor allele

MAF

rs4592338

10

56098424

PCDH15

1.21

0.0027

16

A

0.04

rs978674

10

56119975

PCDH15

1.17

0.0032

16

A

0.04

rs7321994

13

46742539

LCP1

−0.53

0.0055

2

A

0.20

rs1787534

18

47445407

MYO5B

0.75

0.0055

1

T

0.09

rs873816

18

46101074

CTIF

−0.59

0.0079

2

C

0.15

rs9567638

13

46754734

LCP1

−1.43

0.0084

3

C

0.02

rs8087713

18

46677185

DYM

0.54

0.011

2

G

0.17

rs10775489

18

46667299

DYM

0.54

0.011

2

A

0.17

rs12959910

18

46337861

CTIF

0.64

0.012

19

G

0.10

rs2296119

13

46729259

LCP1

−0.49

0.015

2

T

0.17

10 most significant SNPs associated with low frequency hearing overall (max n = 4970)

SNP

Chromosome

Base Position

Gene

Effect Size (dB)

p-value

LD Block

Minor allele

MAF

rs10492452

13

46721562

LCP1

0.45

0.00056

1

A

0.20

rs16951446

18

47599093

MYO5B

−0.73

0.0017

1

G

0.05

rs16951488

18

47610821

MYO5B

−0.73

0.0017

1

G

0.05

rs16913796

10

55659824

PCDH15

−0.59

0.003

3

T

0.08

rs6561296

13

46702401

LCP1

0.38

0.0033

1

C

0.21

rs9316187

13

46713702

LCP1

0.33

0.0079

1

A

0.24

rs6432974

2

167982976

XIRP2

0.39

0.0097

5

T

0.14

rs1937389

10

56319852

PCDH15

0.37

0.01

24

G

0.16

rs11003924

10

55662156

PCDH15

−0.44

0.01

4

T

0.11

rs11003925

10

55662226

PCDH15

−0.44

0.01

4

T

0.11

10 most significant SNPs associated with low frequency hearing in males (max n = 2445)

SNP

Chromosome

Base Position

Gene

Effect Size (dB)

p-value

LD Block

Minor allele

MAF

rs1877192

2

167863420

XIRP2

0.69

0.0017

3

C

0.12

rs12571150

10

56546055

PCDH15

−0.51

0.0022

29

T

0.25

rs16951446

18

47599093

MYO5B

−0.89

0.0062

1

G

0.05

rs16951488

18

47610821

MYO5B

−0.89

0.0062

1

G

0.05

rs1912985

10

56538759

PCDH15

0.53

0.0068

28

T

0.16

rs10492452

13

46721562

LCP1

0.48

0.008

1

A

0.20

rs1317355

18

46379626

CTIF

0.45

0.0086

24

T

0.23

rs877885

18

46241163

CTIF

0.42

0.0097

13

A

0.26

rs11662494

18

46241017

CTIF

−0.51

0.0098

13

T

0.15

rs937023

18

46383785

CTIF

0.41

0.011

25

C

0.28

10 most significant SNPs associated with low frequency hearing in females (max n = 2525)

SNP

Chromosome

Base Position

Gene

Effect Size (dB)

p-value

LD Block

Minor allele

MAF

rs7233521

18

46219733

CTIF

0.98

0.00047

11

A

0.09

rs9567638

13

46754734

LCP1

−1.76

0.0011

3

C

0.02

rs7321994

13

46742539

LCP1

−0.55

0.0039

2

A

0.20

rs11003876

10

55594049

PCDH15

0.45

0.004

1

C

0.43

rs11003889

10

55623229

PCDH15

0.49

0.0057

1

C

0.27

rs1937389

10

56319852

PCDH15

0.58

0.006

24

G

0.16

rs2296119

13

46729259

LCP1

−0.55

0.0062

2

T

0.17

rs4478893

10

55635024

PCDH15

0.43

0.0087

2

G

0.34

rs1900425

10

55638740

PCDH15

0.42

0.0093

3

A

0.34

rs8087713

18

46677185

DYM

0.54

0.01

2

G

0.17

  1. LD block refers to the numbered LD blocks that were calculated using a solid spine of LD in Haploview. Effect size is reported per copy of minor allele in the SNP, and represents the number of decibels (dB) higher or lower for the hearing threshold of children with the minor allele. A positive effect size represents a decreased hearing threshold and a negative effect size represents enhanced hearing. Some SNPs are below the maximum n because not all SNPs in our study were generated for each child. MAF = minor allele frequency