Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups

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

doi:10.1186/s12920-021-00921-2

Table 2 Effect allele frequencies (EAFs) of intraocular pressure related single nucleotide polymorphisms in East Asian groups including Koreans

From: Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups

SNP ID	Chr	Position	Type	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
rs1013278	chr7	117603820	Intergenic	G	C	CTTNBP2;LSM8	0.1	0.105	0.000	0.118	0.162	0.076	− 0.079
rs10281637	chr7	116151338	Intergenic	T	C	CAV2;CAV1	0.0089	0.005	0.000	0.011	0.061	0.015	0.079
rs10483727	chr14	61072875	Intergenic	T	C	SIX6;SALRNA1	0.21	0.167	− 0.381	0.113	− 5.663	0.202	− 0.034
rs10505100	chr8	108278616	Intronic	C	A	ANGPT1	0.23	0.233	0.000	0.156	− 0.852	0.182	− 0.142
rs10918274	chr1	165714416	Intronic	T	C	TMCO1	0.99	0.976	− 0.046	1.000	0.175	0.990	0.000
rs11217878	chr11	120340383	Intronic	G	A	ARHGEF12	0.24	0.224	0.000	0.339	1.234	0.227	0.000
rs113985657	chr6	597203	Intronic	C	T	EXOC2	0.14	0.167	0.000	0.097	− 0.467	0.086	− 0.448
rs11710139	chr3	150059342	Intergenic	G	A	LINC01214;TSC22D2	0.075	0.071	0.000	0.038	− 0.586	0.045	− 0.137
rs12377624	chr9	129373110	Intergenic	G	C	MVB12B;LMX1B	0.13	0.114	0.000	0.140	0.048	0.131	0.000
rs1254276	chr14	60847001	Intergenic	C	T	LINC02322;C14orf39	0.78	0.833	0.126	0.887	1.936	0.778	0.000
rs12699251	chr7	11679113	Intronic	A	G	THSD7A	0.2	0.224	0.000	0.215	0.061	0.167	− 0.079
rs1579050	chr2	153364527	Intronic	A	G	FMNL2	0.026	0.010	0.000	0.054	0.658	0.030	0.034
rs17752199	chr6	51406848	Intergenic	A	G	TFAP2B;PKHD1	0.12	0.105	0.000	0.145	0.280	0.106	− 0.054
rs1874458	chr16	65080739	Intronic	G	A	CDH11	0.21	0.229	0.000	0.177	− 0.186	0.182	− 0.079
rs2022945	chr8	108251139	Intergenic	A	G	ABRA;ANGPT1	0.77	0.762	0.000	0.828	0.586	0.813	0.096
rs2024211	chr7	116153025	Intergenic	A	C	CAV2;CAV1	0.0089	0.005	0.000	0.011	0.061	0.015	0.079
rs2073006	chr6	637465	Intronic	C	T	EXOC2	0.15	0.181	0.046	0.118	− 0.447	0.081	− 2.070
rs2188836	chr7	117635382	Intergenic	C	T	CTTNBP2;LSM8	0.09	0.076	0.000	0.113	0.182	0.066	− 0.079
rs2317961	chr6	1533116	Intergenic	A	G	FOXF2;FOXCUT	0.51	0.519	0.000	0.500	− 0.023	0.495	− 0.009
rs2472493	chr9	107695848	Intergenic	G	A	ABCA1;SLC44A1	0.49	0.471	0.000	0.543	0.945	0.455	− 0.170
rs2472496	chr9	107695353	Intergenic	G	A	ABCA1;SLC44A1	0.47	0.457	0.000	0.538	0.544	0.449	− 0.034
rs2487032	chr9	107703934	Intergenic	G	A	ABCA1;SLC44A1	0.49	0.467	0.000	0.532	0.198	0.449	− 0.079
rs2745572	chr6	1548369	Intergenic	A	G	FOXF2;FOXCUT	0.49	0.481	0.000	0.505	0.137	0.510	0.079
rs28500712	chr4	7896213	Intronic	A	G	AFAP1	0.68	0.695	0.000	0.640	− 0.198	0.657	− 0.041
rs28520091	chr4	7846240	Intronic	C	T	AFAP1	0.29	0.329	0.000	0.328	0.199	0.313	0.041
rs28795989	chr4	7891545	Intronic	A	G	AFAP1	0.18	0.181	0.000	0.156	− 0.155	0.187	0.000
rs2935057	chr6	170454915	Intergenic	A	G	LINC00574;LOC102724511	0.76	0.700	− 0.155	0.774	0.054	0.783	0.054
rs3013274	chr6	170464367	Intergenic	G	A	LINC00574;LOC102724511	0.5	0.419	− 0.286	0.565	0.497	0.556	0.142
rs31918	chr5	14820927	Intronic	C	T	ANKH	0.33	0.319	0.000	0.344	0.046	0.298	− 0.079
rs327716	chr7	80838977	Intergenic	A	G	SEMA3C;LOC105369146	0.91	0.919	0.000	0.909	0.000	0.909	0.000
rs33912345	chr14	60976537	Exonic	C	A	SIX6	0.21	0.167	− 0.046	0.113	− 1.659	0.212	0.000
rs3785176	chr16	8896931	Intronic	A	C	PMM2	0.28	0.271	0.000	0.296	0.061	0.237	− 0.079
rs4141671	chr10	60338753	Intronic	T	C	BICC1	0.48	0.443	0.000	0.441	− 0.182	0.439	− 0.079
rs4236601	chr7	116162729	Intergenic	G	A	CAV2;CAV1	0.0099	0.005	0.000	0.016	0.172	0.015	0.079
rs55892100	chr7	115810676	Intergenic	A	G	TFEC;TES	0.8	0.805	0.000	0.785	− 0.061	0.803	0.000
rs5756813	chr22	38175477	Intergenic	G	T	TRIOBP;H1F0	0.71	0.724	0.000	0.849	2.955	0.717	0.000
rs58073046	chr11	120248493	Intronic	A	G	ARHGEF12	0.17	0.167	0.000	0.215	0.447	0.167	0.000
rs61394862	chr5	14851094	Intronic	C	T	ANKH	0.32	0.319	0.000	0.323	0.000	0.298	− 0.041
rs6478746	chr9	129367398	Intergenic	G	A	MVB12B;LMX1B	0.97	0.976	0.000	0.946	− 0.945	0.944	− 0.944
rs66602224	chr8	108293718	Intronic	G	A	ANGPT1	0.14	0.167	0.000	0.075	− 0.945	0.131	0.000
rs6732795	chr2	69411517	Intronic	A	C	ANTXR1	0.85	0.819	0.000	0.823	− 0.175	0.869	0.040
rs73174345	chr3	169252883	Intronic	T	G	MECOM	0	0.000	0.000	0.000	0.000	0.000	0.000
rs746491	chr11	86406159	Intergenic	C	A	ME3;PRSS23	0.14	0.129	0.000	0.086	− 0.715	0.096	− 0.170
rs7518099	chr1	165736880	Intronic	C	T	TMCO1	0.99	0.976	− 0.046	1.000	0.175	0.990	0.000
rs7555523	chr1	165718979	Intronic	C	A	TMCO1	0.99	0.976	− 0.046	1.000	0.175	0.990	0.000
rs7924522	chr11	128380742	Intronic	C	A	ETS1	0.86	0.876	0.000	0.742	− 2.617	0.859	0.000
rs8141433	chr22	19854006	Intergenic	A	G	GNB1L;TXNRD2	0.037	0.033	0.000	0.022	− 0.175	0.020	− 0.079
rs9284802	chr3	85095766	Intronic	G	A	CADM2	0.17	0.152	0.000	0.134	− 0.215	0.172	0.000
rs945686	chr9	129378026	Intronic	G	C	LMX1B	0.99	0.995	0.000	0.989	0.000	0.980	− 0.079
rs9494457	chr6	136474794	Intronic	T	A	PDE7B	0.33	0.262	− 0.381	0.328	0.000	0.439	2.084
rs9853115	chr3	186131600	Intergenic	T	A	DGKG;LINC02052	0.73	0.752	0.000	0.753	0.169	0.753	0.079
rs9913911	chr17	10031183	Intronic	A	G	GAS7	0.5	0.519	0.000	0.522	0.175	0.414	− 2.084

SNP ID	Chr	Position	Type	Ref Allele	Alt Allele	Nearby/containing Gene	CHB EAF	CHB log₁₀ P	JPT EAF	JPT log₁₀ P	KOR EAF	KOR log₁₀ P
rs1013278	chr7	117603820	Intergenic	G	C	CTTNBP2;LSM8	0.126	0.216	0.087	− 0.081	0.114	0.413
rs10281637	chr7	116151338	Intergenic	T	C	CAV2;CAV1	0.015	0.133	0.000	− 0.232	0.007	− 0.169
rs10483727	chr14	61072875	Intergenic	T	C	SIX6;SALRNA1	0.316	4.865	0.260	1.092	0.271	3.218
rs10505100	chr8	108278616	Intronic	C	A	ANGPT1	0.272	0.285	0.303	0.819	0.283	2.435
rs10918274	chr1	165714416	Intronic	T	C	TMCO1	0.995	0.059	0.995	0.047	0.993	0.229
rs11217878	chr11	120340383	Intronic	G	A	ARHGEF12	0.189	− 0.328	0.231	− 0.023	0.227	− 0.229
rs113985657	chr6	597203	Intronic	C	T	EXOC2	0.189	0.430	0.144	0.004	0.208	4.434
rs11710139	chr3	150059342	Intergenic	G	A	LINC01214;TSC22D2	0.097	0.195	0.120	0.779	0.096	0.939
rs12377624	chr9	129373110	Intergenic	G	C	MVB12B;LMX1B	0.146	0.078	0.125	− 0.004	0.079	− 4.387
rs1254276	chr14	60847001	Intergenic	C	T	LINC02322;C14orf39	0.689	− 1.099	0.745	− 0.295	0.727	− 2.493
rs12699251	chr7	11679113	Intronic	A	G	THSD7A	0.184	− 0.059	0.207	0.023	0.229	0.876
rs1579050	chr2	153364527	Intronic	A	G	FMNL2	0.029	0.038	0.010	− 0.343	0.025	− 0.017
rs17752199	chr6	51406848	Intergenic	A	G	TFAP2B;PKHD1	0.112	− 0.059	0.115	− 0.023	0.103	− 0.624
rs1874458	chr16	65080739	Intronic	G	A	CDH11	0.228	0.078	0.212	0.000	0.250	1.588
rs2022945	chr8	108251139	Intergenic	A	G	ABRA;ANGPT1	0.733	− 0.195	0.702	− 0.779	0.723	− 2.027
rs2024211	chr7	116153025	Intergenic	A	C	CAV2;CAV1	0.015	0.133	0.000	− 0.232	0.007	− 0.169
rs2073006	chr6	637465	Intronic	C	T	EXOC2	0.189	0.430	0.183	0.440	0.220	4.434
rs2188836	chr7	117635382	Intergenic	C	T	CTTNBP2;LSM8	0.107	0.133	0.091	0.000	0.095	0.098
rs2317961	chr6	1533116	Intergenic	A	G	FOXF2;FOXCUT	0.549	0.195	0.466	− 0.313	0.475	− 0.904
rs2472493	chr9	107695848	Intergenic	G	A	ABCA1;SLC44A1	0.519	0.285	0.447	− 0.685	0.460	− 0.711
rs2472496	chr9	107695353	Intergenic	G	A	ABCA1;SLC44A1	0.485	0.059	0.438	− 0.203	0.428	− 1.306
rs2487032	chr9	107703934	Intergenic	G	A	ABCA1;SLC44A1	0.510	0.059	0.505	0.047	0.476	− 0.209
rs2745572	chr6	1548369	Intergenic	A	G	FOXF2;FOXCUT	0.451	− 0.430	0.519	0.346	0.517	0.624
rs28500712	chr4	7896213	Intronic	A	G	AFAP1	0.752	0.489	0.649	− 0.191	0.709	0.767
rs28520091	chr4	7846240	Intronic	C	T	AFAP1	0.214	− 0.598	0.279	− 0.025	0.295	0.076
rs28795989	chr4	7891545	Intronic	A	G	AFAP1	0.184	0.035	0.188	0.035	0.170	− 0.196
rs2935057	chr6	170454915	Intergenic	A	G	LINC00574;LOC102724511	0.733	− 0.133	0.793	0.236	0.729	− 0.913
rs3013274	chr6	170464367	Intergenic	G	A	LINC00574;LOC102724511	0.379	− 1.458	0.587	0.867	0.428	− 3.235
rs31918	chr5	14820927	Intronic	C	T	ANKH	0.316	− 0.051	0.375	0.339	0.334	0.054
rs327716	chr7	80838977	Intergenic	A	G	SEMA3C;LOC105369146	0.942	0.285	0.904	− 0.025	0.947	3.495
rs33912345	chr14	60976537	Exonic	C	A	SIX6	0.311	1.376	0.255	0.351	0.268	2.976
rs3785176	chr16	8896931	Intronic	A	C	PMM2	0.267	− 0.052	0.322	0.329	0.316	1.128
rs4141671	chr10	60338753	Intronic	T	C	BICC1	0.519	0.195	0.529	0.339	0.489	0.113
rs4236601	chr7	116162729	Intergenic	G	A	CAV2;CAV1	0.015	0.133	0.000	− 0.779	0.007	− 0.229
rs55892100	chr7	115810676	Intergenic	A	G	TFEC;TES	0.772	− 0.133	0.841	0.346	0.835	1.552
rs5756813	chr22	38175477	Intergenic	G	T	TRIOBP;H1F0	0.728	0.059	0.529	− 4.121	0.643	− 3.218
rs58073046	chr11	120248493	Intronic	A	G	ARHGEF12	0.155	− 0.059	0.159	− 0.035	0.168	− 0.023
rs61394862	chr5	14851094	Intronic	C	T	ANKH	0.301	− 0.059	0.365	0.339	0.333	0.196
rs6478746	chr9	129367398	Intergenic	G	A	MVB12B;LMX1B	0.971	0.000	0.990	1.200	0.967	− 0.106
rs66602224	chr8	108293718	Intronic	G	A	ANGPT1	0.189	0.430	0.144	0.004	0.204	4.208
rs6732795	chr2	69411517	Intronic	A	C	ANTXR1	0.825	− 0.133	0.894	0.489	0.900	3.633
rs73174345	chr3	169252883	Intronic	T	G	MECOM	0.000	0.000	0.000	0.000	0.000	0.000
rs746491	chr11	86406159	Intergenic	C	A	ME3;PRSS23	0.180	0.285	0.221	1.329	0.193	3.194
rs7518099	chr1	165736880	Intronic	C	T	TMCO1	0.995	0.059	0.995	0.047	0.993	0.229
rs7555523	chr1	165718979	Intronic	C	A	TMCO1	0.995	0.059	0.995	0.047	0.993	0.229
rs7924522	chr11	128380742	Intronic	C	A	ETS1	0.859	0.000	0.933	1.329	0.907	3.495
rs8141433	chr22	19854006	Intergenic	A	G	GNB1L;TXNRD2	0.029	− 0.059	0.077	1.092	0.040	0.113
rs9284802	chr3	85095766	Intronic	G	A	CADM2	0.150	− 0.099	0.255	1.296	0.176	0.106
rs945686	chr9	129378026	Intronic	G	C	LMX1B	0.990	0.000	1.000	0.339	0.987	− 0.169
rs9494457	chr6	136474794	Intronic	T	A	PDE7B	0.340	0.051	0.284	− 0.530	0.282	− 1.983
rs9853115	chr3	186131600	Intergenic	T	A	DGKG;LINC02052	0.757	0.195	0.654	− 1.329	0.701	− 0.768
rs9913911	chr17	10031183	Intronic	A	G	GAS7	0.466	− 0.285	0.572	1.376	0.554	2.055

Chr: chromosome, EAF: effect allele frequency, ref allele: reference allele, alt allele: alterative allele, 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, P-value: adjusted Fischer’s test, statistical significance was set at P < 0.05 and |log₁₀ P|> 1.301

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