rs2165241

plus

Geno	Mag	Summary
(C;C)	0	normal
(C;T)	2.2	4.4x increased risk of exfoliation glaucoma
(T;T)	2.3	>10x increased risk of exfoliation glaucoma

Reference

GRCh38 38.1/141

Chromosome

15

Position

73929861

Gene	LOXL1, LOXL1-AS1

is a	snp
is	mentioned by
dbSNP	rs2165241
dbSNP (classic)	rs2165241
ClinGen	rs2165241
ebi	rs2165241
HLI	rs2165241
Exac	rs2165241
Gnomad	rs2165241
Varsome	rs2165241
LitVar	rs2165241
Map	rs2165241
PheGenI	rs2165241
Biobank	rs2165241
1000 genomes	rs2165241
hgdp	rs2165241
ensembl	rs2165241
geneview	rs2165241
scholar	rs2165241
google	rs2165241
pharmgkb	rs2165241
gwascentral	rs2165241
openSNP	rs2165241
23andMe	rs2165241
SNPshot	rs2165241
SNPdbe	rs2165241
MSV3d	rs2165241
GWAS Ctlg	rs2165241

GMAF

0.3136

Max Magnitude

2.3

?

(C;C) (C;T) (T;T)

28

This SNP, located in an intron of the LOXL1 gene, was initially reported to be associated with exfoliation glaucoma. However, it was shown in the same study to no longer be significant once two other SNPs, which cause actual changes in the LOXL1 protein, were identified.

More specifically, the risk allele rs2165241(T) was found to be associated with glaucoma only because it effectively predicted (with 90% probability) the actual high-risk haplotype consisting of rs1048661(G) and rs3825942(C), as oriented with respect to their entries in dbSNP. [PMID 17690259]

However, a meta-analysis published in 2010 concluded that it's likely that SNPs rs1048661 and rs2165241 are not directly implicated in the pathogenesis of glaucoma; only the nearby rs3825942 seemed to be the disease-associated SNP.[PMID 20142848 ]

[PMID 18287813] rs2165241 was significantly associated with XFG and XFS (p=4.13x10e-9 for an additive model, heterozygote odds ratio = 4.42 (CI: 2.3-8.5), homozygote odds ratio = 34.19 (CI: 4.48-261), with the rs2165241 (T) allele being the risk allele, found in 83.1% of cases versus 52.4% in controls, based on a study of 62 Caucasian patients. Significant association was also found for rs3825942 (p=1.89x10e-6).

[PMID 18385788 ] rs1048661 (G), rs3825942 (G), and rs2165241 (T) are highly associated with XFS and XFG in American and European populations. The GGT haplotype constitutes a major risk haplotype for exfoliation.

[PMID 18385063] Confirmed as risk for pseudoexfoliation (PEX) and pseudoexfoliation glaucoma (PEXG) in populations of German and Italian descent.

Rs2165241
PubMed	[PMID 17690259]
Affy Probeset	SNP_A-8476188
Affy Orientation	reverse
On GW 5.0	0
Alleles A/B	A/G
Ancestral	C
Population	EU(Scand.)
Allele	T
Case Freq.
Control Freq.
Odds Ratio Het
Odds Ratio Hom
Odds Ratio All	1.96
Disease	Glaucoma (GC)

rs2165241 increases susceptibility to Exfoliation glaucoma 3.62 times for carriers of the T allele [PMID 17690259]

rs2165241 increases susceptibility to Glaucoma 1.96 times for carriers of the T allele [PMID 17690259]

rs2165241 increases susceptibility to Primary open-angle glaucoma 1.04 times for carriers of the T allele [PMID 17690259]

OMIM	153456
Desc	LYSYL OXIDASE-LIKE 1; LOXL1
Variant
Related	also

[PMID 19936304 ] Evaluation of LOXL1 polymorphisms in exfoliation syndrome in a Chinese population

[PMID 20051886 ] Lack of Association of Polymorphisms in Elastin With Pseudoexfoliation Syndrome and Glaucoma

OMIM	153456
Desc
Variant	0003
Related	also

OMIM	177650
Desc
Variant
Related	also

[PMID 21510775 ] Lack of association between LOXL1 gene polymorphisms and primary open angle glaucoma in the Saudi Arabian population

[PMID 21970694] Prevalence of high-risk alleles in the LOXL1 gene and its association with pseudoexfoliation syndrome and exfoliation glaucoma in a Latin American population

[PMID 22194657 ] Analysis of LOXL1 gene variants in Japanese patients with branch retinal vein occlusion

[PMID 22765198] TT polymorphism in rs2165241 and rs1048661 region in lysyl oxidase like-1 gene may have a role in stress urinary incontinence physiopathology

[PMID 18223248] The LOXL1 gene variations are not associated with primary open-angle and primary angle-closure glaucomas.

[PMID 18254956 ] DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity.

[PMID 18334928 ] Analysis of LOXL1 polymorphisms in a United States population with pseudoexfoliation glaucoma.

[PMID 18334947 ] Association of non-synonymous single nucleotide polymorphisms in the LOXL1 gene with pseudoexfoliation syndrome in India.

[PMID 18421074 ] Lack of association between LOXL1 variants and primary open-angle glaucoma in three different populations.

[PMID 18450598] Association of LOXL1 gene polymorphisms with pseudoexfoliation in the Japanese.

[PMID 18618003 ] Exfoliation syndrome and exfoliation glaucoma-associated LOXL1 variations are not involved in pigment dispersion syndrome and pigmentary glaucoma.

[PMID 18648524 ] Evaluation of LOXL1 polymorphisms in eyes with exfoliation glaucoma in Japanese.

[PMID 18958304 ] LOXL1 variants in elderly Japanese patients with exfoliation syndrome/glaucoma, primary open-angle glaucoma, normal tension glaucoma, and cataract.

[PMID 19098994 ] Evaluation of LOXL1 polymorphisms in primary open-angle glaucoma in southern and northern Chinese.

[PMID 19112534 ] Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma.

[PMID 19343041] Association of LOXL1 gene with Finnish exfoliation syndrome patients.

[PMID 19503743 ] Association of LOXL1 polymorphisms with pseudoexfoliation in the Chinese.

[PMID 19801603 ] Rapid inexpensive genome-wide association using pooled whole blood.

[PMID 20431720 ] Major LOXL1 risk allele is reversed in exfoliation glaucoma in a black South African population.

[PMID 20661439 ] Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus.

[PMID 21150032 ] Complex genetic mechanisms in glaucoma: an overview.

[PMID 21559813] No association of LOXL1 gene polymorphisms with Alzheimer's disease.

[PMID 23441117 ] Evaluation of lysyl oxidase-like 1 gene polymorphisms in pseudoexfoliation syndrome in a Korean population

[PMID 23869164 ] Association of lysyl oxidase-like 1 gene common sequence variants in Greek patients with pseudoexfoliation syndrome and pseudoexfoliation glaucoma

[PMID 24068861 ] The T allele of lysyl oxidase-like 1 rs41435250 is a novel risk factor for pseudoexfoliation syndrome and pseudoexfoliation glaucoma independently and through intragenic epistatic interaction

[PMID 24603551 ] Association between Polymorphisms in Lysyl Oxidase-Like 1 and Susceptibility to Pseudoexfoliation Syndrome and Pseudoexfoliation Glaucoma

[PMID 24892565] Association of lysyl oxidase-like 1 gene polymorphisms in pseudoexfoliation syndrome and pseudoexfoliation glaucoma in a Spanish population

[PMID 24893574] Genetic polymorphism related to exfoliative glaucoma is also associated with primary open-angle glaucoma risk

[PMID 24967207 ] Lack of association between lysyl oxidase-like 1 polymorphisms and primary open angle glaucoma: a meta-analysis

[PMID 25304275] LOXL1 Gene Polymorphism With Exfoliation Syndrome/Exfoliation Glaucoma: A Meta-Analysis

[PMID 25709925 ] The association of LOXL1 polymorphisms with exfoliation syndrome/glaucoma: Meta-analysis

[PMID 26319397 ] LOXL1 gene variants and their association with pseudoexfoliation glaucoma (XFG) in Spanish patients

[PMID 30405941 ] Three Single Nucleotide Polymorphisms of LOXL1' in a Turkish Population with Pseudoexfoliation Syndrome and Pseudoexfoliation Glaucoma.