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

Harrison, Sean; Lewis, Sarah J.; Hall, Amanda J.; Vuckovic, Dragana; Girotto, Giorgia; Martin, Richard M.; Adams, Josephine C.

doi:10.1186/s12920-015-0112-2

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

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

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ISSN: 1755-8794

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