Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups

Shin, Hyun-Tae; Yoon, Byung Woo; Seo, Je Hyun

doi:10.1186/s12886-021-01830-9

Table 2 Effect allele frequencies (EAFs) of 31 late age-related macular degeneration related single nucleotide polymorphisms in East Asian groups including Koreans

From: Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups

SNP ID	Chr	Position	Function	Ref allele	Alt allele	Nearby/containing Gene	Global East Asian EAF	CHS EAF	CHS log₁₀ P	CDX EAF	CDX log₁₀ P	KHV EAF	KHV log₁₀ P	CHB EAF	CHB log₁₀ P	JPT EAF	JPT log₁₀ P	KOR EAF	KOR log₁₀ P
rs10033900	chr4	110,659,067	intergenic	T	C	CFI	0.39	0.39	0.00	0.45	0.92	0.43	0.65	0.31	−1.72	0.37	−0.24	0.34	−2.17
rs10781182	chr9	76,617,720	intergenic	T	G	MIR6130/RORB	0.49	0.51	0.01	0.54	0.50	0.49	0.02	0.50	0.00	0.41	−0.81	0.41	−3.69
rs10922109	chr1	196,704,632	intronic	C	A	CFH	0.44	0.46	0.00	0.51	0.67	0.40	−0.27	0.38	−0.57	0.47	0.19	0.47	0.89
rs11080055	chr17	26,649,724	intronic	A	C	TMEM97/VTN	0.72	0.80	0.77	0.63	−1.03	0.63	−0.99	0.74	0.08	0.77	0.54	0.76	1.50
rs1142	chr7	104,756,326	downstream	C	T	KMT2E/SRPK2	0.37	0.35	0.00	0.47	1.03	0.39	0.20	0.37	0.00	0.26	−1.61	0.34	−1.03
rs11884770	chr2	228,086,920	ncRNA_intronic	T	C	COL4A3	0.78	0.78	0.00	0.81	0.28	0.84	0.72	0.76	−0.13	0.73	−0.56	0.76	−0.43
rs12019136	chr19	5,835,677	intronic	G	A	C3	0.14	0.08	−0.69	0.29	4.20	0.21	0.99	0.10	−0.42	0.04	−3.29	0.08	−6.61
rs12357257	chr10	24,999,593	intronic	G	A	ARHGAP21	0.05	0.02	−0.65	0.11	1.37	0.08	0.47	0.02	−0.79	0.03	−0.35	0.03	−1.70
rs13081855	chr3	99,481,539	ncRNA_intronic	G	T	COL8A1/FILIP1L	0.05	0.04	−0.01	0.05	0.00	0.07	0.35	0.05	0.06	0.03	−0.22	0.03	−2.17
rs1626340	chr9	101,923,372	intergenic	G	A	TGFBR1/COL15A1	0.46	0.38	−0.69	0.53	0.67	0.38	−0.72	0.50	0.37	0.52	0.60	0.51	2.17
rs181705462	chr6	31,947,027	intronic	G	T	C2/CFB/SKIV2L	0.00	0.00	0.00	0.00	0.00	0.01	0.20	0.01	0.40	0.00	0.00	0.00	−0.13
rs2043085	chr15	58,680,954	intergenic	T	C	AQP9;LIPC	0.50	0.55	0.35	0.52	0.13	0.55	0.35	0.52	0.13	0.38	−1.85	0.48	−0.43
rs2230199	chr19	6,718,387	exonic	G	C	C3	0.00	0.00	−0.67	0.00	−0.75	0.01	0.20	0.01	0.79	0.00	−0.81	0.00	− 0.93
rs2740488	chr9	107,661,742	intronic	A	C	ABCA1	0.24	0.26	0.01	0.25	0.02	0.20	−0.35	0.22	−0.13	0.29	0.55	0.26	0.45
rs3138141	chr12	56,115,778	ncRNA_intronic	C	A	RDH5/CD63/MMP19	0.12	0.12	0.00	0.16	0.66	0.19	0.99	0.09	−0.33	0.04	−2.42	0.07	−5.43
rs3750846	chr10	124,215,565	intronic	T	C	ARMS2/HTRA1	0.41	0.39	−0.01	0.40	0.00	0.41	0.00	0.43	0.08	0.40	0.00	0.42	0.14
rs429358	chr19	45,411,941	exonic	T	C	APOE	0.09	0.06	−0.29	0.10	0.22	0.09	0.08	0.10	0.13	0.08	0.00	0.09	0.18
rs55975637	chr3	99,419,853	ncRNA_intronic	G	A	COL8A1	0.06	0.06	0.00	0.06	0.02	0.09	0.45	0.05	0.00	0.03	−0.53	0.03	−3.03
rs570618	chr1	196,657,064	intronic	T	G	CFH	0.95	0.96	0.01	0.98	0.66	0.96	0.11	0.93	−0.42	0.93	−0.35	0.92	−2.17
rs5754227	chr22	33,105,817	intronic	T	C	SYN3/TIMP3	0.61	0.63	0.01	0.55	−0.57	0.65	0.21	0.56	−0.40	0.67	0.62	0.67	2.97
rs61818925	chr1	196,815,450	intergenic	T	G	CFHR1	0.41	0.33	−0.69	0.32	−0.92	0.48	0.70	0.46	0.37	0.46	0.46	0.50	5.24
rs61985136	chr14	68,769,199	intronic	C	T	RAD51B	0.45	0.40	−0.26	0.51	0.59	0.49	0.27	0.38	−0.75	0.47	0.16	0.42	−0.93
rs62247658	chr3	64,715,155	ncRNA_intronic	C	T	ADAMTS9-AS2	0.24	0.25	0.00	0.31	0.75	0.31	0.78	0.19	−0.42	0.17	− 0.81	0.20	−1.70
rs6565597	chr17	79,526,821	intronic	C	T	NPLOC4/TSPAN10	0.21	0.17	−0.36	0.24	0.24	0.23	0.15	0.18	−0.15	0.22	0.01	0.21	0.03
rs67538026	chr19	1,031,438	intronic	C	T	CNN2	0.52	0.47	−0.29	0.57	0.46	0.49	−0.20	0.44	−0.79	0.62	1.12	0.50	−0.64
rs72802342	chr16	75,234,872	intergenic	C	A	CTRB2/CTRB1	0.13	0.12	0.00	0.20	1.03	0.16	0.30	0.11	−0.13	0.09	−0.65	0.11	−0.75
rs73036519	chr19	45,748,362	intergenic	G	C	EXOC3L2/MARK4	0.00	0.00	0.00	0.00	0.00	0.01	0.27	0.00	0.00	0.00	0.00	0.00	−0.35
rs7803454	chr7	99,991,548	intronic	C	T	PILRB/PILRA	0.03	0.03	0.00	0.02	−0.23	0.06	0.72	0.01	−0.40	0.03	0.00	0.02	−0.40
rs8135665	chr22	38,476,276	intronic	C	T	SLC16A8	0.14	0.09	−1.02	0.23	2.55	0.19	0.99	0.10	−0.79	0.10	−0.81	0.10	−2.17
rs943080	chr6	43,826,627	intergenic	C	T	VEGFA	0.73	0.73	0.00	0.76	0.37	0.79	0.99	0.72	−0.06	0.67	−0.92	0.67	−2.46
rs9564692	chr13	31,821,240	intronic	C	T	B3GALTL	0.71	0.71	0.00	0.73	0.14	0.73	0.20	0.70	−0.06	0.69	−0.20	0.73	0.63

CHS Southern Han Chinese, China, CDX Chinese Dai in Xishuangbanna, China, KHV Kinh in Ho Chi Minh City, Vietnam, CHB: Han Chinese in Beijing, China, JPT Japanese in Tokyo in 1000 genome project, KOR Korean Reference Genome data base, Chr chromosome, EAF effect allele frequency, ref. allele reference allele, alt allele alterative allele, P-value: adjusted Fischer’s test assuming 138 hypotheses, statistical significance was set at P < 0.05

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