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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