Table 4.

Summary statistics of UMODL1 SNPs in follow-up study (cases defined as spherical equivalent ≤ −10.0 diopters)

			Allele†		Genotype counts (11/12/22)		Minor allele freq		Association test (best result)‡
SNP*		Location*	1	2	Controls	Cases	Controls	Cases	Pasym	Model	Pemp
Follow-up study (Sample Set 2)
rs220168	S47	Intron	A	G	220/138/22	179/712/12	0.2395	0.1813	0.0074	Dominant	0.0568
rs220170	S48	Intron	C	T	228/120/22	178/70/15	0.2216	0.1901	0.1173	Dominant	0.5556
rs11911271	S49	Intron	T	C	205/157/27	138/117/14	0.2712	0.2695	0.7241	Dominant	0.9536
rs3819142	S54	Exon (ns)	A	C	215/149/20	182/76/10	0.2461	0.1791	0.0021	Dominant	0.0168
Combined analysis (Sample Sets 1 and 2)
rs220168	S47	Intron	A	G	436/251/43	291/149/24	0.2308	0.2123	0.2883	Allelic	0.8884
rs220170	S48	Intron	C	T	439/243/41	294/145/27	0.2248	0.2135	0.4118	Dominant	0.9691
rs11911271	S49	Intron	T	C	380/305/54	256/183/32	0.2794	0.2622	0.3194	Dominant	0.9242
rs3819142	S54	Exon (ns)	A	C	420/279/39	294/154/23	0.2419	0.2123	0.0574	Dominant	0.3303

*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 S47 to S49 and S52 as explained in the footnote to Table 2. The non-synonymous (ns) SNP rs3819142 (S54) is located in exon.

†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.