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 1 Effect allele frequencies (EAFs) of intraocular pressure related single nucleotide polymorphisms in populations of diverse ancestry 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 EAF	AMR EAF	AMR log₁₀ P	AFR EAF	AFR log₁₀ P	EAS EAF
rs1013278	chr7	117603820	Intergenic	G	C	CTTNBP2;LSM8	0.31	0.28	− 0.735	0.33	0.738	0.1
rs10281637	chr7	116151338	Intergenic	T	C	CAV2;CAV1	0.22	0.21	− 0.177	0.4	36.671	0.0089
rs10483727	chr14	61072875	Intergenic	T	C	SIX6;SALRNA1	0.35	0.66	51.990	0.034	− 146.666	0.21
rs10505100	chr8	108278616	Intronic	C	A	ANGPT1	0.16	0.18	0.569	0.11	− 5.368	0.23
rs10918274	chr1	165714416	Intronic	T	C	TMCO1	0.92	0.87	− 3.857	0.92	0.000	0.99
rs11217878	chr11	120340383	Intronic	G	A	ARHGEF12	0.21	0.15	− 3.286	0.25	2.601	0.24
rs113985657	chr6	597203	Intronic	C	T	EXOC2	0.12	0.11	− 0.249	0.087	− 3.132	0.14
rs11710139	chr3	15005942	Intergenic	G	A	LINC01214;TSC22D2	0.16	0.14	− 0.578	0.16	0.010	0.075
rs12377624	chr9	129373110	Intergenic	G	C	MVB12B;LMX1B	0.23	0.24	0.194	0.11	− 23.178	0.13
rs1254276	chr14	60847001	Intergenic	C	T	LINC02322;C14orf39	0.63	0.32	− 51.921	0.89	82.782	0.78
rs12699251	chr7	11679113	Intronic	A	G	THSD7A	0.25	0.35	6.518	0.11	− 29.965	0.2
rs1579050	chr2	153364527	Intronic	A	G	FMNL2	0.28	0.46	19.037	0.1	− 46.833	0.026
rs17752199	chr6	51406848	Intergenic	A	G	TFAP2B;PKHD1	0.13	0.13	0.000	0.15	1.166	0.12
rs1874458	chr16	65080739	Intronic	G	A	CDH11	0.2	0.21	0.187	0.085	− 24.499	0.21
rs2022945	chr8	108251139	Intergenic	A	G	ABRA;ANGPT1	0.84	0.83	− 0.204	0.9	7.594	0.77
rs2024211	chr7	116153025	Intergenic	A	C	CAV2;CAV1	0.21	0.2	− 0.177	0.34	20.570	0.0089
rs2073006	chr6	637465	Intronic	C	T	EXOC2	0.11	0.12	0.258	0.045	− 13.535	0.15
rs2188836	chr7	117635382	Intergenic	C	T	CTTNBP2;LSM8	0.33	0.28	− 1.730	0.39	4.233	0.09
rs2317961	chr6	1533116	Intergenic	A	G	FOXF2;FOXCUT	0.63	0.59	− 1.121	0.82	40.735	0.51
rs2472493	chr9	107695848	Intergenic	G	A	ABCA1;SLC44A1	0.61	0.65	1.095	0.69	6.970	0.49
rs2472496	chr9	107695353	Intergenic	G	A	ABCA1;SLC44A1	0.61	0.64	0.690	0.69	6.970	0.47
rs2487032	chr9	107703934	Intergenic	G	A	ABCA1;SLC44A1	0.6	0.48	− 7.836	0.83	58.058	0.49
rs2745572	chr6	1548369	Intergenic	A	G	FOXF2;FOXCUT	0.36	0.38	0.395	0.15	− 52.096	0.49
rs28500712	chr4	7896213	Intronic	A	G	AFAP1	0.66	0.59	− 3.016	0.72	4.381	0.68
rs28520091	chr4	7846240	Intronic	C	T	AFAP1	0.32	0.38	2.332	0.15	− 36.294	0.29
rs28795989	chr4	7891545	Intronic	A	G	AFAP1	0.29	0.32	0.743	0.14	− 30.033	0.18
rs2935057	chr6	170454915	Intergenic	A	G	LINC00574;LOC102724511	0.8	0.82	0.502	0.74	− 5.373	0.76
rs3013274	chr6	170464367	Intergenic	G	A	LINC00574;LOC102724511	0.61	0.58	− 0.664	0.7	8.654	0.5
rs31918	chr5	14820927	Intronic	C	T	ANKH	0.29	0.34	1.752	0.28	− 0.298	0.33
rs327716	chr7	80838977	Intergenic	A	G	SEMA3C;LOC105369146	0.71	0.68	− 0.743	0.81	12.896	0.91
rs33912345	chr14	60976537	Exonic	C	A	SIX6	0.34	0.66	54.967	0.032	− 143.370	0.21
rs3785176	chr16	8896931	Intronic	A	C	PMM2	0.18	0.14	− 1.712	0.096	− 13.535	0.28
rs4141671	chr10	60338753	Intronic	T	C	BICC1	0.49	0.32	− 15.716	0.55	3.871	0.48
rs4236601	chr7	116162729	Intergenic	G	A	CAV2;CAV1	0.23	0.21	− 0.434	0.4	32.449	0.0099
rs55892100	chr7	115810676	Intergenic	A	G	TFEC;TES	0.54	0.43	− 6.518	0.61	5.149	0.8
rs5756813	chr22	38175477	Intergenic	G	T	TRIOBP;H1F0	0.55	0.62	2.799	0.4	− 21.169	0.71
rs58073046	chr11	120248493	Intronic	A	G	ARHGEF12	0.1	0.042	− 6.316	0.013	− 32.104	0.17
rs61394862	chr5	14851094	Intronic	C	T	ANKH	0.28	0.33	1.781	0.26	− 0.777	0.32
rs6478746	chr9	129367398	Intergenic	G	A	MVB12B;LMX1B	0.8	0.85	2.421	0.73	− 6.990	0.97
rs66602224	chr8	108293718	Intronic	G	A	ANGPT1	0.32	0.32	0.000	0.44	14.831	0.14
rs6732795	chr2	69411517	Intronic	A	C	ANTXR1	0.66	0.49	− 16.002	0.78	16.515	0.85
rs73174345	chr3	169252883	Intronic	T	G	MECOM	0.054	0.036	− 1.095	0.13	18.287	0
rs746491	chr11	86406159	Intergenic	C	A	ME3;PRSS23	0.15	0.17	0.588	0.11	− 3.715	0.14
rs7518099	chr1	165736880	Intronic	C	T	TMCO1	0.92	0.87	− 3.857	0.91	− 0.608	0.99
rs7555523	chr1	165718979	Intronic	C	A	TMCO1	0.9	0.87	− 1.399	0.85	− 6.009	0.99
rs7924522	chr11	128380742	Intronic	C	A	ETS1	0.75	0.71	− 1.291	0.79	2.503	0.86
rs8141433	chr22	19854006	Intergenic	A	G	GNB1L;TXNRD2	0.28	0.16	− 10.572	0.69	159.128	0.037
rs9284802	chr3	85095766	Intronic	G	A	CADM2	0.32	0.33	0.177	0.13	− 46.150	0.17
rs945686	chr9	129378026	Intronic	G	C	LMX1B	0.82	0.87	2.585	0.73	− 11.619	0.99
rs9494457	chr6	136474794	Intronic	T	A	PDE7B	0.39	0.45	2.158	0.37	− 0.696	0.33
rs9853115	chr3	186131600	Intergenic	T	A	DGKG;LINC02052	0.56	0.47	− 4.386	0.48	− 6.471	0.73
rs9913911	chr17	10031183	Intronic	A	G	GAS7	0.31	0.32	0.177	0.16	− 28.132	0.5

SNP ID	Chr	Position	Type	Ref Allele	Alt Allele	Nearby/containing Gene	EAS log₁₀ P	SAS EAF	SAS log₁₀ P	EUR EAF	EUR log₁₀ P	KOR EAF	KOR log₁₀ P
rs1013278	chr7	117603820	Intergenic	G	C	CTTNBP2;LSM8	− 47.563	0.4	6.676	0.4	7.043	0.114	− 102.924
rs10281637	chr7	116151338	Intergenic	T	C	CAV2;CAV1	− 80.906	0.19	− 1.271	0.26	2.100	0.007	− 232.094
rs10483727	chr14	61072875	Intergenic	T	C	SIX6;SALRNA1	− 17.809	0.42	4.030	0.6	47.063	0.271	− 13.494
rs10505100	chr8	108278616	Intronic	C	A	ANGPT1	6.644	0.2	2.350	0.11	− 4.159	0.283	40.539
rs10918274	chr1	165714416	Intronic	T	C	TMCO1	20.362	0.96	5.017	0.86	− 7.783	0.993	62.418
rs11217878	chr11	120340383	Intronic	G	A	ARHGEF12	1.395	0.23	0.659	0.16	− 3.413	0.227	1.147
rs113985657	chr6	597203	Intronic	C	T	EXOC2	1.036	0.12	0.000	0.14	1.014	0.208	26.399
rs11710139	chr3	150059342	Intergenic	G	A	LINC01214;TSC22D2	− 12.606	0.16	0.000	0.23	6.403	0.096	− 16.719
rs12377624	chr9	129373110	Intergenic	G	C	MVB12B;LMX1B	− 12.549	0.33	9.258	0.37	18.120	0.079	− 78.578
rs1254276	chr14	60847001	Intergenic	C	T	LINC02322;C14orf39	19.784	0.6	− 0.943	0.4	− 39.746	0.727	19.784
rs12699251	chr7	11679113	Intronic	A	G	THSD7A	− 3.064	0.25	0.000	0.4	19.691	0.229	− 1.524
rs1579050	chr2	153364527	Intronic	A	G	FMNL2	− 89.083	0.35	4.372	0.58	69.618	0.025	− 242.856
rs17752199	chr6	51406848	Intergenic	A	G	TFAP2B;PKHD1	− 0.364	0.12	− 0.327	0.12	− 0.320	0.103	− 3.773
rs1874458	chr16	65080739	Intronic	G	A	CDH11	0.314	0.2	0.000	0.33	17.034	0.250	7.076
rs2022945	chr8	108251139	Intergenic	A	G	ABRA;ANGPT1	− 6.644	0.8	− 2.350	0.89	4.159	0.723	− 37.209
rs2024211	chr7	116153025	Intergenic	A	C	CAV2;CAV1	− 76.273	0.19	− 0.664	0.26	3.118	0.007	− 218.926
rs2073006	chr6	637465	Intronic	C	T	EXOC2	3.236	0.11	0.000	0.13	1.060	0.220	40.976
rs2188836	chr7	117635382	Intergenic	C	T	CTTNBP2;LSM8	− 60.936	0.43	7.936	0.41	5.477	0.095	− 150.366
rs2317961	chr6	1533116	Intergenic	A	G	FOXF2;FOXCUT	− 11.567	0.52	− 8.961	0.64	0.217	0.475	− 44.116
rs2472493	chr9	107695848	Intergenic	G	A	ABCA1;SLC44A1	− 11.416	0.65	1.567	0.58	− 1.060	0.460	− 40.945
rs2472496	chr9	107695353	Intergenic	G	A	ABCA1;SLC44A1	− 15.152	0.67	3.051	0.58	− 1.060	0.428	− 59.932
rs2487032	chr9	107703934	Intergenic	G	A	ABCA1;SLC44A1	− 9.692	0.56	− 1.474	0.5	− 7.924	0.476	− 28.298
rs2745572	chr6	1548369	Intergenic	A	G	FOXF2;FOXCUT	13.501	0.48	10.620	0.36	0.000	0.517	45.723
rs28500712	chr4	7896213	Intronic	A	G	AFAP1	0.586	0.54	− 10.735	0.72	3.416	0.709	5.547
rs28520091	chr4	7846240	Intronic	C	T	AFAP1	− 1.186	0.37	2.314	0.5	25.369	0.295	− 1.770
rs28795989	chr4	7891545	Intronic	A	G	AFAP1	− 12.655	0.26	− 1.084	0.6	73.748	0.170	− 36.886
rs2935057	chr6	170454915	Intergenic	A	G	LINC00574;LOC102724511	− 2.238	0.84	2.252	0.88	8.761	0.729	− 13.364
rs3013274	chr6	170464367	Intergenic	G	A	LINC00574;LOC102724511	− 9.753	0.68	4.063	0.57	− 1.606	0.428	− 59.784
rs31918	chr5	14820927	Intronic	C	T	ANKH	1.881	0.22	− 4.799	0.29	0.000	0.334	4.776
rs327716	chr7	80838977	Intergenic	A	G	SEMA3C;LOC105369146	45.585	0.64	− 4.367	0.43	− 60.462	0.947	183.742
rs33912345	chr14	60976537	Exonic	C	A	SIX6	− 15.632	0.4	3.083	0.6	50.841	0.268	− 11.500
rs3785176	chr16	8896931	Intronic	A	C	PMM2	11.463	0.13	− 3.575	0.25	6.099	0.316	45.623
rs4141671	chr10	60338753	Intronic	T	C	BICC1	− 0.226	0.56	3.867	0.49	0.000	0.489	− 0.037
rs4236601	chr7	116162729	Intergenic	G	A	CAV2;CAV1	− 84.231	0.19	− 1.952	0.26	1.262	0.007	− 244.996
rs55892100	chr7	115810676	Intergenic	A	G	TFEC;TES	54.802	0.43	− 8.650	0.37	− 21.708	0.835	182.195
rs5756813	chr22	38175477	Intergenic	G	T	TRIOBP;H1F0	20.456	0.5	− 2.095	0.58	0.989	0.643	16.731
rs58073046	chr11	120248493	Intronic	A	G	ARHGEF12	8.745	0.21	17.513	0.1	0.000	0.168	18.725
rs61394862	chr5	14851094	Intronic	C	T	ANKH	1.910	0.21	− 4.971	0.28	0.000	0.333	6.636
rs6478746	chr9	129367398	Intergenic	G	A	MVB12B;LMX1B	50.342	0.78	− 0.668	0.7	− 10.654	0.967	127.390
rs66602224	chr8	108293718	Intronic	G	A	ANGPT1	− 32.704	0.28	− 1.639	0.4	5.548	0.204	− 31.901
rs6732795	chr2	69411517	Intronic	A	C	ANTXR1	34.845	0.68	0.540	0.4	− 50.841	0.900	152.394
rs73174345	chr3	169252883	Intronic	T	G	MECOM	− 21.410	0.014	− 7.882	0.059	0.230	0.000	− 59.854
rs746491	chr11	86406159	Intergenic	C	A	ME3;PRSS23	− 0.338	0.13	− 0.815	0.21	5.097	0.193	6.653
rs7518099	chr1	165736880	Intronic	C	T	TMCO1	20.362	0.96	5.017	0.86	− 7.783	0.993	63.362
rs7555523	chr1	165718979	Intronic	C	A	TMCO1	27.970	0.96	9.258	0.86	− 3.391	0.993	85.262
rs7924522	chr11	128380742	Intronic	C	A	ETS1	14.150	0.75	0.000	0.63	− 13.128	0.907	78.316
rs8141433	chr22	19854006	Intergenic	A	G	GNB1L;TXNRD2	− 78.658	0.22	− 3.655	0.15	− 18.042	0.040	− 200.793
rs9284802	chr3	85095766	Intronic	G	A	CADM2	− 22.155	0.41	6.585	0.63	72.241	0.176	− 49.830
rs945686	chr9	129378026	Intronic	G	C	LMX1B	61.221	0.79	− 1.348	0.76	− 4.495	0.987	156.676
rs9494457	chr6	136474794	Intronic	T	A	PDE7B	− 3.323	0.44	2.158	0.37	− 0.570	0.282	− 23.733
rs9853115	chr3	186131600	Intergenic	T	A	DGKG;LINC02052	23.247	0.57	0.193	0.53	− 1.014	0.701	38.881
rs9913911	chr17	10031183	Intronic	A	G	GAS7	28.572	0.27	− 1.662	0.37	3.416	0.554	109.722

Chr: chromosome EAF: effect allele frequency ref allele: reference allele alt allele: alterative allele AMR: Americans AFR: Africans, EAS: East Asians, SAS: South Asians, EUR: Europeans, KOR: Koreans, P-value: adjusted Fischer’s test, statistical significance was set at P < 0.05 and |log₁₀ P|> 1.301

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