Investigating the relationship between UMODL1 gene polymorphisms and high myopia: a case–control study in Chinese

Zhu, Miao-miao; Yap, Maurice KH; Ho, Daniel WH; Fung, Wai Yan; Ng, Po Wah; Gu, Yang-shun; Yip, Shea Ping

doi:10.1186/1471-2350-13-64

Table 2 Summary statistics of UMODL1 SNPs in initial study (cases defined as spherical equivalent ≤ −8.0 diopters)

From: Investigating the relationship between UMODL1 gene polymorphisms and high myopia: a case–control study in Chinese

			Allele†		Genotype counts (11/12/22)		Minor allele freq		Association test (best result)‡
SNP*		Location*	1	2	Controls	Cases	Controls	Cases	P _asym	Model	P _emp
rs220260	S1	Intergenic	C	G	149/157/44	155/160/36	0.3500	0.3343	0.3630	Recessive	1
rs220262	S2	Intergenic	A	T	174/148/29	173/157/22	0.2934	0.2855	0.3038	Recessive	1
rs220263	S3	Intergenic	A	G	106/159/83	85/179/86	0.4670	0.4986	0.0673	Dominant	0.9882
rs220265	S4	Intergenic	C	A	127/155/62	106/181/65	0.4055	0.4418	0.0572	Dominant	0.9763
rs12627387	S5	Intergenic	G	A	100/166/86	104/184/66	0.4801	0.4463	0.0614	Recessive	0.9829
rs13340012	S6	Intergenic	A	C	211/117/22	201/134/14	0.2300	0.2321	0.1738	Recessive	1
rs220271	S7	Intron	C	T	128/164/61	135/175/45	0.4051	0.3732	0.0860	Recessive	0.9955
rs220276	S8	Intron	G	A	118/168/66	129/168/52	0.4261	0.3897	0.1650	Allelic	1
rs220278	S9	Intron	G	A	143/157/53	159/153/42	0.3725	0.3347	0.1374	Allelic	0.9997
rs220281	S10	Intron	G	A	157/151/44	149/169/38	0.3395	0.3441	0.4408	Genotypic	1
rs220282	S11	Intron	G	A	139/160/55	126/160/64	0.3814	0.4114	0.2487	Allelic	1
rs220285	S12	Intron	C	G	252/69/11	269/78/7	0.1370	0.1299	0.2740	Recessive	1
rs220298	S13	Intron	G	A	156/159/39	181/144/31	0.3347	0.2893	0.0647	Allelic	0.9867
rs220299	S14	Intron	T	C	156/152/46	141/168/43	0.3446	0.3608	0.2804	Dominant	1
rs8133951	S15	Intron	G	A	126/151/51	135/159/48	0.3857	0.3728	0.5810	Recessive	1
rs749020	S16	Intron	G	A	112/166/76	112/166/75	0.4492	0.4476	0.9425	Recessive	1
rs220301	S17	Intron	G	C	136/156/60	134/166/50	0.3920	0.3800	0.3145	Recessive	1
rs2839466	S18	Intron	G	A	136/165/48	147/160/43	0.3739	0.3514	0.3803	Additive	1
rs220308	S19	Intron	T	G	105/169/80	111/168/74	0.4647	0.4476	0.5187	Allelic	1
rs220109	S20	Exon (syn)	C	T	112/153/83	114/167/72	0.4583	0.4405	0.2706	Recessive	1
rs220110	S21	Intron	C	A	159/141/52	149/154/46	0.3480	0.3524	0.5088	Dominant	1
rs12626854	S22	Intron	T	C	156/156/41	149/156/40	0.3371	0.3420	0.7891	Dominant	1
rs220120	S23	Intron	G	C	165/150/37	180/136/34	0.3182	0.2914	0.2276	Dominant	1
rs220131	S24	Intron	C	T	86/177/79	97/171/83	0.4898	0.4801	0.4574	Dominant	1
rs220136	S25	Intron	C	A	90/185/76	92/169/87	0.4801	0.4928	0.2953	Recessive	1
rs11701944	S26	Intron	A	G	144/152/48	133/169/46	0.3605	0.3750	0.3282	Dominant	1
rs220140	S27	Intron	C	G	161/156/38	164/161/31	0.3268	0.3132	0.3686	Recessive	1
rs220143	S28	Intron	G	A	177/140/35	183/143/23	0.2983	0.2708	0.1071	Recessive	0.9990
rs2839468	S29	Intron	A	C	111/161/82	100/179/72	0.4590	0.4601	0.3391	Genotypic	1
rs220145	S30	Intron	G	A	224/105/18	204/135/17	0.2032	0.2374	0.0489	Dominant	0.9569
rs13047454	S31	Intron	A	G	183/138/34	175/160/19	0.2901	0.2797	0.0331	Recessive	0.8971
rs220148	S32	Intron	A	C	167/146/39	182/140/28	0.3182	0.2800	0.1182	Allelic	0.9995
rs220149	S33	Intron	T	G	96/165/86	96/185/71	0.4856	0.4645	0.1439	Recessive	0.9999
rs220153	S34	Intron	G	A	212/108/27	199/125/23	0.2334	0.2464	0.3153	Dominant	1
rs220154	S35	Intron	C	T	109/163/77	109/178/64	0.4542	0.4359	0.2066	Recessive	1
rs220155	S36	Intron	C	T	136/144/58	125/162/55	0.3846	0.3977	0.3229	Dominant	1
rs11910495	S37	Intron	A	G	256/90/8	250/92/9	0.1497	0.1567	0.7161	Allelic	1
rs13051533	S38	Intron	G	A	169/136/40	163/147/34	0.3130	0.3125	0.4684	Recessive	1
rs220157	S39	Intron	C	T	126/156/64	121/175/47	0.4104	0.3921	0.0870	Recessive	0.9957
rs9984766	S40	Intron	G	A	226/86/21	204/98/16	0.1922	0.2044	0.3168	Dominant	1
rs220158	S41	Exon (syn)	C	T	214/117/23	225/104/24	0.2302	0.2153	0.3677	Dominant	1
rs220159	S42	Exon (ns)	G	A	136/153/64	120/177/54	0.3980	0.4060	0.1664	Genotypic	1
rs2839470	S43	Intron	C	T	123/163/57	125/168/55	0.4038	0.3994	0.7717	Recessive	1
rs4920063	S44	Intron	G	A	155/139/47	133/184/36	0.3416	0.3626	0.0100	Genotypic	0.9219
rs220161	S45	Intron	C	G	92/158/83	106/171/67	0.4865	0.4433	0.0879	Recessive	0.9963
rs2839471	S46	Intron	T	C	98/178/76	97/187/70	0.4688	0.4619	0.5512	Recessive	1
rs220168	S47	Intron	A	G	217/113/21	198/132/21	0.2208	0.2479	0.1447	Dominant	0.9999
rs220170	S48	Intron	C	T	212/123/19	199/130/23	0.2274	0.2500	0.3192	Allelic	1
rs11911271	S49	Intron	T	C	176/148/27	201/122/31	0.2877	0.2599	0.0773	Dominant	0.9929
rs220171	S50	Intron	C	T	158/163/30	185/137/30	0.3177	0.2798	0.0455	Dominant	0.9477
rs220172	S51	Intron	G	A	171/137/34	160/139/35	0.2997	0.3129	0.5858	Dominant	1
rs220173	S52	Intron	C	G	88/183/84	97/180/79	0.4944	0.4747	0.4535	Additive	1
rs3819141	S53	Exon (syn)	T	A	128/163/62	120/160/73	0.4065	0.4334	0.2925	Recessive	1
rs3819142	S54	Exon (ns)	A	C	206/130/19	206/130/19	0.2366	0.2514	0.5125	Additive	1
rs220179	S55	Intron	C	T	175/146/27	175/146/27	0.2874	0.2963	0.7097	Additive	1
rs915840	S56	Intron	T	C	212/122/21	212/122/21	0.2310	0.2486	0.3025	Dominant	1
rs220181	S57	Intron	G	A	183/140/15	183/140/15	0.2515	0.2536	0.2039	Recessive	1

*SNPs are listed down the column in sequential order from the 5’ end to the 3’ end of the sense strand of the UMODL1 gene. They are also designated as S1 to S57 for the sake of easy referencing. SNPs located in exons are either synonymous (syn) or non-synonymous (ns).
†1: major allele; 2: minor allele.
‡Single-marker analysis is performed with Plink. Asymptotic P values (P _asym) are obtained by chi-square test, and empirical P values (P _emp) obtained by 10,000 permutations for correcting multiple comparisons. The genetic models tested for each SNP are allelic, genotypic, additive (tested by trend test), dominant and recessive. Here, only the best result and the corresponding genetic model are shown for each SNP.

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ISSN: 1471-2350

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