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Table 5 Effect sizes of SNPs in CTIF or LCP1 for averaged high or low frequency hearing compared between ALSPAC and G-EAR

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

CTIF: 10 most significant SNPs in high frequency tests overall
SNP Minor Allele Major allele ALSPAC MAF ALSPAC Effect Size (dB) ALSPAC p-value G-EAR Effect Size (rank normal) G-EAR p-value LD Block
rs12959910 G A 0.11 0.61 0.0008 0.096 0.11 19
rs8085434 C T 0.05 0.84 0.002 0.081 0.27 8
rs8091955 G A 0.45 0.34 0.004 0.045 0.22 22
rs1994559 A G 0.17 0.43 0.004 0.059 0.23 19
rs1319946 C T 0.49 0.31 0.007 0.040 0.24 22
rs1317625 A G 0.22 0.30 0.026 −0.021 0.59 25
rs7233521 A G 0.09 0.43 0.031 0.069 0.35 11
rs1316826 C T 0.31 0.26 0.032 0.059 0.17 21
rs4583322 A G 0.35 0.25 0.032 0.008 0.82 19
rs937021 G A 0.44 0.23 0.039 −0.043 0.21 25
CTIF: 10 most significant SNPs in high frequency tests in males
SNP Minor Allele Major allele ALSPAC MAF ALSPAC Effect Size (dB) ALSPAC p-value G-EAR Effect Size (rank normal) G-EAR p-value LD Block
rs2337069 T C 0.22 0.58 0.004 0.010 0.26 3
rs8085434 C T 0.05 1.04 0.009 0.002 0.89 8
rs11662494 T C 0.15 −0.57 0.012 0.001 0.91 13
rs937021 G A 0.45 0.37 0.026 0.003 0.74 25
rs12959910 G A 0.11 0.57 0.030 0.021 0.10 19
rs7227797 G A 0.31 0.38 0.033 0.014 0.07 3
rs1994559 A G 0.18 0.44 0.040 0.002 0.82 19
rs11082695 A G 0.17 −0.43 0.048 0.001 0.95 13
rs8091955 G A 0.46 0.32 0.058 0.014 0.08 22
rs1319946 C T 0.50 0.32 0.060 0.009 0.20 22
CTIF: 10 most significant SNPs in high frequency tests in females
SNP Minor Allele Major allele ALSPAC MAF ALSPAC Effect Size (dB) ALSPAC p-value G-EAR Effect Size (rank normal) G-EAR p-value LD Block
rs873816 C T 0.15 −0.59 0.008 −0.003 0.69 2
rs12959910 G A 0.10 0.64 0.012 −0.007 0.55 19
rs8091955 G A 0.45 0.33 0.036 0.001 0.86 22
rs4939781 G A 0.21 −0.40 0.040 −0.009 0.20 2
rs11082698 G A 0.46 0.32 0.043 −0.008 0.18 14
rs1317625 A G 0.21 0.38 0.047 −0.001 0.83 25
rs4939804 A G 0.23 0.36 0.053 −0.004 0.60 14
rs11662760 A G 0.09 −0.53 0.056 −0.006 0.58 1
rs7233521 A G 0.09 0.54 0.058 −0.028 0.04 11
rs1319946 C T 0.49 0.30 0.062 −0.001 0.90 22
LCP1: 10 most significant SNPs in low frequency tests overall
SNP Minor Allele Major allele ALSPAC MAF ALSPAC Effect Size (dB) ALSPAC p-value G-EAR Effect Size (rank normal) G-EAR p-value LD Block
rs10492452 A C 0.20 0.45 0.0006 −0.009 0.86 1
rs6561296 C T 0.21 0.38 0.003 −0.013 0.79 1
rs9316187 A G 0.24 0.33 0.008 0.007 0.87 1
rs1409437 G A 0.44 −0.23 0.029 −0.066 0.08 1
rs2146880 A C 0.45 0.23 0.030 0.025 0.52 1
rs1886040 C T 0.49 0.22 0.039 0.028 0.47 1
rs2093707 A C 0.49 0.21 0.046 0.034 0.37 1
rs7321994 A G 0.20 −0.24 0.067 −0.047 0.25 2
rs2209093 C T 0.17 −0.25 0.074 −0.071 0.09 2
rs2296119 T C 0.17 −0.25 0.076 −0.032 0.46 2
LCP1: 10 most significant SNPs in low frequency tests in males
SNP Minor Allele Major allele ALSPAC MAF ALSPAC Effect Size (dB) ALSPAC p-value G-EAR Effect Size (rank normal) G-EAR p-value LD Block
rs10492452 A C 0.20 0.48 0.008 −0.004 0.67 1
rs6561296 C T 0.21 0.40 0.026 −0.006 0.48 1
rs9316187 A G 0.24 0.37 0.031 −0.004 0.63 1
rs1409437 G A 0.44 −0.30 0.039 0.003 0.60 1
rs2146880 A C 0.45 0.26 0.072 −0.001 0.89 1
rs1886040 C T 0.49 0.26 0.075 −0.003 0.56 1
rs2093707 A C 0.49 0.25 0.081 −0.003 0.66 1
rs17601960 C T 0.08 −0.36 0.168 0.043 0.01 3
rs9567638 C T 0.02 0.59 0.246 0.024 0.48 3
rs10492449 G T 0.33 0.14 0.373 −0.006 0.33 3
LCP1: 10 most significant SNPs in low frequency tests in females
SNP Minor Allele Major allele ALSPAC MAF ALSPAC Effect Size (dB) ALSPAC p-value G-EAR Effect Size (rank normal) G-EAR p-value LD Block
rs9567638 C T 0.02 −1.76 0.0011 0.021 0.53 3
rs7321994 A G 0.20 −0.55 0.004 0.006 0.19 2
rs2296119 T C 0.17 −0.55 0.006 0.005 0.35 2
rs2209093 C T 0.17 −0.50 0.012 0.005 0.27 2
rs10492452 A C 0.21 0.43 0.026 0.003 0.64 1
rs2209092 G A 0.22 −0.37 0.042 0.006 0.17 2
rs6561296 C T 0.22 0.36 0.056 0.004 0.55 1
rs9316187 A G 0.24 0.29 0.110 0.007 0.25 1
rs2146880 A C 0.45 0.20 0.202 0.000 0.97 1
rs1886040 C T 0.49 0.18 0.247 0.003 0.55 1
  1. LD block refers to the numbered LD blocks that were calculated using a solid spine of LD in Haploview. The effect allele in G-EAR was the same as in ALSPAC, but the effect sizes in G-EAR were calculated using a rank normal transformation (see Methods) and so cannot be compared directly with the effect sizes from ALSPAC. MAF = minor allele frequency in ALSPAC
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