rs6672420

This is a variant in the RUNX3 gene that changes a isoleucine to an asparagine.

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GWAS Catalog Trait Associations (9)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

skin disease

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele A
OR 0.05
p 2.0e-12
N 404,034
Major Consortium StudyLarge GWAS
multi-ancestry

psoriasis, type 2 diabetes mellitus

Patrick MT et al. “Causal Relationship and Shared Genetic Loci between Psoriasis and Type 2 Diabetes through Trans-Disease Meta-Analysis.” The Journal of Investigative Dermatology 141(6):1493-1502 (2021)
Allele T
OR 1.07
p 3.0e-12
N 925,490
Meta-analysisLarge GWAS
European

Eczematoid dermatitis

Grosche S et al. “Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.” Nature Communications 12(1):6618 (2021)
Allele T
OR 1.08
p 5.0e-12
N 400,449
Large GWAS
European

multiple sclerosis

“Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility.” Science (new York, N.y.) 365(6460) (2019)
Allele A
OR 1.06
p 1.0e-9
N 41,505
Large GWAS
multi-ancestry

atopic eczema

Pasanen A et al. “Identifying Atopic Dermatitis Risk Loci in 1,094,060 Individuals with Subanalysis of Disease Severity and Onset.” The Journal of Investigative Dermatology 144(11):2417-2425 (2024)
Allele A
OR 0.05
p 4.0e-9
N 1,094,060
Large GWAS
multi-ancestry

dermatitis

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele A
OR 0.04
p 2.0e-13
N 391,439
Major Consortium StudyLarge GWAS
European

psoriasis

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele A
OR 0.10
p 5.0e-19
N 629,965
Major Consortium StudyLarge GWAS
multi-ancestry

psoriasis vulgaris

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele A
OR 0.12
p 7.0e-10
N 655,669
Large GWAS
multi-ancestry
Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele A
OR 0.10
p 2.0e-19
N 444,887
Major Consortium StudyLarge GWAS
European
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ClinVar annotation

Benign★☆☆☆
1 submitter1 publication

not specified

View on ClinVar →
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Research that mentions this SNP (1)

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Replication study and meta-analysis indicate a suggestive association of RUNX3 locus with primary biliary cholangitis
Meta-analysisN=9,794Jawed R. et al.(2020)· Immunogenetics

This replication and meta-analysis study examined the association between the RUNX3 locus and primary biliary cholangitis (PBC) in Han Chinese. The tag SNP rs7529070 showed suggestive association with PBC in a meta-analysis of 2553 cases and 7241 controls (p = 1.7 × 10⁻⁴, OR = 1.18, 95% CI = 1.08-1.28). Rs7529070 was in complete linkage disequilibrium with rs4648889, which is known to regulate RUNX3 expression. The study also demonstrated significantly increased RUNX3 expression in PBC patients compared to controls and in a PBC mouse model, suggesting increased RUNX3 expression may promote PBC pathogenesis.

Traits studied:Primary biliary cholangitisPrimary biliary cirrhosis
PubMedDOIMetascience Observatory

About RUNX3

This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

View all RUNX3 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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