Table 1.

Independent SNPs Significantly Associated (p < 5 × 10⁻⁸) with the Two Phenotypes Regarding Hearing Ability in the UK Biobank Discovery Sample

Chr	SNP	EA	EAF	INFO	β	SE	p Value	pJ-Value	Nearest Gene	Distance to Gene (bp)	Other Genes within 100 kb
Hearing Difficulty GWAS
22	rs36062310	G	0.96	1.000	−0.0315	0.003	1.90E−22	1.92E−22	KLHDC7B	0	SYCE3, ADM2, ARSA,aCHKB, CPT1B, LMF2, MAPK8IP2, MIOX, NCAPH2, ODF3B, SBF1, SCO2, SYCE3, TYMP
5	rs6453022	C	0.50	1.000	−0.0126	0.001	1.70E−21	2.07E−12	ARHGEF28	0	–
6	rs759016271	AGTAGTCCACTTTTCTTCTTTGCCTG	0.39	0.997	−0.0127	0.001	6.10E−21	6.16E−21	ZNF318	0	CRIP3, SLC22A7, CUL9, DNPH1, TTBK1
5	rs6890164	A	0.51	0.993	0.0119	0.001	3.30E−19	4.15E−10	ARHGEF28	6177	–
11	rs7951935	G	0.62	0.996	−0.0114	0.001	7.80E−17	7.85E−17	TYR	1472	NOX4
6	rs35186928	G	0.62	0.991	−0.0109	0.001	1.70E−15	1.69E−15	HLA-DQA1	13352	HLA-DRB1, HLA-DRB3, HLA-DRB5, HLA-DRB6
6	rs9493627	G	0.68	1.000	−0.0104	0.001	1.40E−13	1.41E−13	EYA4a	0	–
22	rs132929	G	0.59	0.999	−0.0098	0.001	2.20E−13	4.61E−13	BAIAP2L2a	0	SLC16A8, PICK1, PLA2G6, POLR2F
22	rs5756795	T	0.54	1.000	−0.0092	0.001	5.10E−12	1.09E−11	TRIOBPa	0	GALR3, GCAT, GGA1,aH1F0, LGALS1, NOL12, PDXP, SH3BP1
14	rs1566129	T	0.41	1.000	0.0091	0.001	1.40E−11	1.37E−11	NID2	0	GNG2, RTRAF
4	rs35414371	T	0.87	0.998	−0.0131	0.002	1.60E−11	1.64E−11	CLRN2a	1965	LAP3, MED28, QDPR
3	3:182069497_TA_T	TA	0.84	0.989	−0.0118	0.002	4.10E−11	4.07E−11	ATP11B	441791	–
11	rs12225399	G	0.65	0.989	−0.009	0.001	8.60E−11	8.67E−11	PHLDB1	0	ARCN1, IFT46, KMT2A, TMEM25, TREH, TTC36
11	rs55635402	A	0.81	0.996	0.0105	0.002	2.90E−10	2.94E−10	TUBa	0	EIF3F, NLRP10, OR10A3, RIC3
16	rs62033400	A	0.61	0.999	0.0085	0.001	2.90E−10	2.95E−10	FTO	0	RPGRIP1L
8	rs13277721	G	0.49	0.992	−0.0083	0.001	3.30E−10	3.35E−10	AGO2	0	PTK2
2	rs62188635	C	0.45	0.988	0.0083	0.001	4.70E−10	4.72E−10	KLF7	50519	–
6	rs2236401	C	0.49	0.997	−0.0081	0.001	9.30E−10	9.38E−10	SYNJ2a	0	SERAC1,aGTF2H5
7	rs4947828	T	0.23	0.999	−0.0096	0.002	1.00E−09	1.02E−09	GRB10	0	–
10	rs6597883	T	0.84	0.989	0.0111	0.002	1.00E−09	1.05E−09	CTBP2	0	–
5	rs34442808	T	0.49	0.992	−0.008	0.001	1.30E−09	1.32E−09	MCTP1, SLF1	0	–
10	rs835267	A	0.53	0.996	0.008	0.001	1.60E−09	1.58E−09	EXOC6	0	CYP26A1, CYP26C1
10	rs4948502	T	0.57	0.995	0.0081	0.001	1.70E−09	5.63E−10	ARID5B	0	–
10	rs10824108	G	0.42	0.999	−0.0079	0.001	3.00E−09	1.24E−08	ADK	0	AP3M1, VCL
1	rs12027345	G	0.57	0.995	0.0079	0.001	3.60E−09	3.64E−09	MAST2	12668	GPBP1L1, MAST2, TMEM69, TMA16P2, GPBP1L1
6	rs217289	G	0.56	0.992	−0.0078	0.001	4.90E−09	4.92E−09	SNAP91	0	–
3	rs13093972	A	0.55	0.992	−0.0078	0.001	5.50E−09	5.56E−09	ZBTB20	121137	–
15	rs62015206	C	0.41	1.000	−0.0078	0.001	7.70E−09	7.76E−09	MAPK6	15613	BCL2L10, GNB5
5	rs10475169	A	0.88	1.000	−0.0117	0.002	9.30E−09	9.37E−09	IRX2	190445	–
17	rs17671352	T	0.38	0.999	0.0078	0.001	1.00E−08	1.43E−08	ACADVL	0	DVL2,aDLG4, ASGR1, CLDN7, CTDNEP1, EIF5A, ELP5, GABARAP, GPS2, NEURL4, PHF23, SLC2A4, YBX2
1	rs7525101	C	0.56	1.000	−0.0075	0.001	1.50E−08	1.45E−08	LMX1Aa	61973	–
17	rs12938775	G	0.50	1.000	0.0075	0.001	1.60E−08	2.25E−08	PAFAH1B1	0	CLUH, RAP1GAP2
8	rs76837345	A	0.93	0.997	−0.0146	0.003	1.90E−08	1.95E−08	CHMP4C	0	IMPA1, SLC10A5, SNX16, ZFAND1
6	rs9366417	G	0.26	0.993	0.0085	0.002	2.10E−08	2.12E−08	SOX4	291019	–
8	rs3890736	G	0.63	0.993	−0.0077	0.001	2.20E−08	2.22E−08	GFRA2	15676	–
10	rs143282422	G	0.99	1.000	−0.0349	0.006	2.40E−08	3.02E−08	CDH23a	0	C10orf105
7	rs9691831	A	0.42	0.995	−0.0074	0.001	3.10E−08	3.11E−08	TMEM213	0	ATP6V0A4,aKIAA1549
11	rs141403654	A	0.98	0.878	−0.0313	0.006	3.50E−08	3.53E−08	AGBL2	0	C1QTNF4, FNBP4, MTCH2, NUP160
18	rs4611552	T	0.78	0.995	−0.0089	0.002	3.60E−08	3.56E−08	CCDC68	9362	–
13	rs12552	A	0.44	0.994	0.0073	0.001	4.80E−08	4.86E−08	OLFM4	0	–
1	rs10927035	C	0.35	0.995	−0.0075	0.001	4.90E−08	4.89E−08	AKT3	0	SDCCAG8
Hearing Aid GWAS
5	rs4597943	G	0.51	0.989	−0.0042	0.001	2.10E−11	2.09E−11	ARHGEF28	0	–
2	rs9677089	A	0.75	0.989	−0.0046	0.001	2.00E−10	1.98E−10	SPTBN1a	0	–
6	rs9321402	G	0.68	0.999	−0.0042	0.001	3.00E−10	3.02E−10	EYA4a	0	–
14	rs1566129	T	0.41	1.000	0.0037	0.001	2.50E−09	2.53E−09	NID2	0	RTRAF
3	rs3915060	C	0.27	0.983	0.004	0.001	9.70E−09	9.70E−09	ILDR1a	0	CD86, SLC15A2
10	rs10901863	C	0.73	0.934	−0.004	0.001	2.60E−08	2.65E−08	CTBP2	0	–
8	rs7823971	C	0.80	0.991	−0.0043	0.001	2.70E−08	2.68E−08	RP11-1102P16.1	0	–

Definition of terms: Chr., chromosome; SNP, single-nucleotide polymorphism; EA, effect allele; EAF, frequency of effect allele in BOLT-LMM; INFO, quality metric, combination of imputation score and dosage confidence; β, effect size from BOLT-LMM approximation to infinitesimal mixed model; SE, standard error of the effect size; p value, infinitesimal mixed-effects model association test p value; pJ-value, p value from a joint analysis of all the selected SNPs; nearest gene, protein-coding gene in closest proximity to SNP; distance to gene (bp), distance in base pairs between SNP and nearest gene, a value of 0 indicates the SNP lies within the gene; other genes within 100 kb, list of genes within 100 kb of the SNP.

^aGenes previously linked to hearing phenotypes in mice or humans. Two SNPs reached genome-wide significance in the HAid analysis that are in close proximity to HLA-DQA1 on chr 6 (Figure 2) but were not present in conditional analysis results.