What you carry at this position in your DNA and what research says about it.
DNA Repair and Gut Health: 8/10 evidence, 13 publications.
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Sample genotype (not yours): G/G
Higher Cancer Risk and Lower IBD Risk
Two copies of the G allele lead to reduced FEN1 expression and less efficient DNA repair, increasing the risk of lung and colorectal cancers while offering some protection against inflammatory bowel disease.
What this genotype means: Reduced FEN1 expression; Higher DNA damage levels; Increased lung and colorectal cancer risk.
Sample genotype (not yours): G/T
Typical Cancer and IBD Risk
One copy of each allele results in intermediate FEN1 expression and typical DNA repair capacity, maintaining average population risks for both cancer and inflammatory bowel disease.
What this genotype means: Intermediate FEN1 expression; Typical DNA repair capacity; Baseline health risks.
Sample genotype (not yours): T/T
Lower Cancer Risk but Higher IBD Risk
Two copies of the T allele allow for higher FEN1 expression and more efficient DNA repair, lowering cancer risk but increasing susceptibility to inflammatory bowel disease.
What this genotype means: Higher FEN1 expression; More efficient DNA repair; Increased risk of inflammatory bowel disease.
Gene function and biological role
Gene Function: The FEN1 gene encodes flap structure-specific endonuclease 1, an essential enzyme involved in DNA replication and repair [1]. It plays a critical role in the base excision repair pathway, which fixes damaged DNA bases caused by radiation, toxins, or oxidation [1] [2]. By removing overhanging DNA flaps during replication, this enzyme helps maintain genomic stability and prevents mutations [1]. Reduced activity or expression of this enzyme can lead to an accumulation of DNA damage, potentially initiating cancer development [2] [3]. Conversely, proper regulation of this pathway is crucial for maintaining cellular health and preventing abnormal cell growth [3].
Variant Impact: The rs4246215 variant is located in the 3 prime UTR of the FEN1 gene, where it influences how the gene is regulated. The G allele creates a binding site for a specific microRNA, hsa-miR-1236-3p, which downregulates FEN1 expression and reduces the amount of DNA repair enzyme produced [1]. This reduction in FEN1 expression leads to higher levels of cellular DNA damage and increases susceptibility to certain cancers [1] [4]. In contrast, the T allele disrupts this microRNA binding site, allowing for higher FEN1 expression and more efficient DNA repair [1]. However, this genetic variation also influences immune responses, with the T allele being associated with an increased risk of inflammatory bowel disease [5].
Key Insight: The G allele allows a specific microRNA to bind and downregulate DNA repair, increasing cancer risk but lowering the risk of inflammatory bowel disease.
Location: FEN1. Chromosome 11 · 11q12.2 · 61.8 Mb
Estimated prevalence by population
Global 51.7%; European 42.4%; African 84.5%; East Asian 19.9%; South Asian 66.3%; Americas 26.0%; Ashkenazi 50.2%; Finnish 30.4%; Middle Eastern 42.7%; Amish 55.8%.
Estimated GG genotype frequency.
Global 37.3%; European 45.4%; African 14.8%; East Asian 49.4%; South Asian 30.2%; Americas 50.0%; Ashkenazi 41.3%; Finnish 49.5%; Middle Eastern 45.3%; Amish 37.8%.
Estimated GT genotype frequency.
Global 11.0%; European 12.2%; African 0.6%; East Asian 30.6%; South Asian 3.4%; Americas 24.0%; Ashkenazi 8.5%; Finnish 20.1%; Middle Eastern 12.0%; Amish 6.4%.
Estimated TT genotype frequency.
Showing effects for G/G genotype
Cancer & Oncology
Colorectal Cancer
Colorectal Cancer. Evidence: 3/10. Source: PMID 31089142. ~1.1x Risk.
Lung Cancer
Lung Cancer. Evidence: 3/10. Source: PMID 19618370. ~1.7x Risk.
Immunity & Inflammation
Chronic Inflammatory Diseases
Inflammatory Bowel Disease. Evidence: 6/10. Source: PMID 23128233. Lower Risk.
Cardiovascular & Metabolic
Lipids & Cholesterol
Blood Lipid Levels. Evidence: 8/10. Source: PMID 34503513. Typical.
Showing effects for G/T genotype
Colorectal Cancer. Evidence: 3/10. Source: PMID 31089142. Typical Risk.
Lung Cancer. Evidence: 3/10. Source: PMID 19618370. Typical Risk.
Inflammatory Bowel Disease. Evidence: 6/10. Source: PMID 23128233. Typical Risk.
Showing effects for T/T genotype
Colorectal Cancer. Evidence: 3/10. Source: PMID 31089142. Lower Risk.
Lung Cancer. Evidence: 3/10. Source: PMID 19618370. Lower Risk.
Inflammatory Bowel Disease. Evidence: 6/10. Source: PMID 23128233. ~1.1x Risk.
What this genotype means for the people who carry it
Sample genotype: GG (Homozygous)
Cells with two G alleles experience reduced expression of the FEN1 DNA repair enzyme because a specific microRNA binds to this site and downregulates its production [1]. This reduction in FEN1 levels impairs the base excision repair pathway, leading to higher levels of accumulated DNA damage [1]. Consequently, clinical studies have linked this genotype to a significantly increased risk of developing lung cancer [1]. It is also associated with a higher susceptibility to colorectal cancer [2]. However, the lower expression of this gene appears to modulate immune pathways in a way that reduces the risk of inflammatory bowel disease [3]. Additionally, this genotype is associated with altered levels of blood lipids, including higher fatty acids and cholesteryl esters [4].
Reduced FEN1 expression; Higher DNA damage levels; Increased lung and colorectal cancer risk.
Sample genotype: GT (Heterozygous)
Possessing one copy of each allele provides a balanced genetic profile with intermediate levels of FEN1 expression. The presence of one G allele allows some microRNA-mediated downregulation, while the T allele maintains baseline DNA repair efficiency [1]. Because of this balance, there is no strong deviation from average population risks for lung or colorectal cancers [1] [2]. Similarly, the risk for inflammatory bowel disease remains at a typical baseline level [3]. Blood lipid and metabolite levels are also generally typical, showing no extreme variations [4]. This genotype represents the most common genetic baseline in many global populations.
Intermediate FEN1 expression; Typical DNA repair capacity; Baseline health risks.
Sample genotype: TT (Homozygous)
Two copies of the T allele prevent the binding of microRNA hsa-miR-1236-3p, resulting in higher expression of the FEN1 DNA repair enzyme [1]. This enhanced expression supports more efficient repair of DNA damage, which significantly lowers the risk of developing lung cancer [1]. It is also associated with a reduced susceptibility to colorectal cancer [2]. However, this genetic setup is linked to a higher risk of inflammatory bowel disease, likely due to the role of DNA repair pathways in gut mucosal immunity [3]. Additionally, this genotype is associated with typical blood lipid levels, though some studies note minor variations in specific phospholipids [4].
Higher FEN1 expression; More efficient DNA repair; Increased risk of inflammatory bowel disease.
Variants with shared genetic architecture
rs174541 · FEN1 Gene · Chr 11 · Type 2 Diabetes Risk
rs267607954 · MSH2 Gene · Chr 2 · Lynch Syndrome Risk
rs397507581 · BRCA2 Gene · Chr 13 · Breast Cancer Risk
Functional FEN1 polymorphisms are associated with DNA damage levels and lung cancer risk.
Base Excision Repair Gene Polymorphisms and Wilms Tumor Susceptibility.
Association analyses identify 31 new risk loci for colorectal cancer susceptibility.
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Content updated August 2026.
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