rs2165241
A SNP in the LOXL1-AS1 gene on chromosome 15. Its most notable genotype is T;T: >10x increased risk of exfoliation glaucoma
- Gene
- LOXL1-AS1
- Location
- Chr 1573,929,861 (GRCh38)
- Highest magnitude
- 2.3Worth knowing
- Tested on
- 23andMe, AncestryDNA, FamilyTreeDNA
- Minor allele frequency
- 31%
Genotypes
As shown in 23andMe and AncestryDNA files.
- C;CGoodnormal
- C;TBad4.4x increased risk of exfoliation glaucoma
- T;TMost notableBad>10x increased risk of exfoliation glaucoma
On SNPedia: (C;C), (C;T), (T;T). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.
Frequency
Share of each genotype in 11 HapMap populations.
- AverageC;C 56% C;T 35% T;T 9%
- European ancestry (Utah)C;C 35% C;T 43% T;T 22%
- Han Chinese (Beijing)C;C 84% C;T 15% T;T <1%
- Japanese (Tokyo)C;C 74% C;T 24% T;T 3%
- Yoruba (Nigeria)C;C 59% C;T 37% T;T 4%
- African ancestry (Southwest US)C;C 61% C;T 30% T;T 9%
- Chinese (Denver)C;C 84% C;T 16% T;T 0%
- Gujarati IndianC;C 40% C;T 46% T;T 15%
- Luhya (Kenya)C;C 68% C;T 30% T;T 2%
- Mexican ancestry (Los Angeles)C;C 31% C;T 53% T;T 16%
- Maasai (Kenya)C;C 56% C;T 39% T;T 5%
- TuscanC;C 26% C;T 54% T;T 21%
Related
Conditions, medicines and genes
Notes
From SNPedia
Show notes, about 320 words
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. 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. 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). 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. Confirmed as risk for pseudoexfoliation (PEX) and pseudoexfoliation glaucoma (PEXG) in populations of German and Italian descent. rs2165241 increases susceptibility to Exfoliation glaucoma 3.62 times for carriers of the T allele rs2165241 increases susceptibility to Glaucoma 1.96 times for carriers of the T allele rs2165241 increases susceptibility to Primary open-angle glaucoma 1.04 times for carriers of the T allele
C;T
glaucoma risk likely to actually be based on nearby rs3825942
T;T
glaucoma risk likely to actually be based on nearby rs3825942
Source and license
Adapted from rs2165241 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.
SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.