rs229527

This is a protein-altering variant in the C1QTNF6 gene.

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GWAS Catalog Trait Associations (6)

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

hypothyroidism

White SL et al. “Global multi-ancestry genome-wide analyses identify genes and biological pathways associated with thyroid cancer and benign thyroid diseases.” Nature Genetics 58(2):307-316 (2026)
Allele A
OR 0.08
p 1.0e-53
N 2,444,128
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 0.05
p 4.0e-15
N 626,411
Major Consortium StudyLarge GWAS
multi-ancestry

Vitiligo

Jin Y et al. “Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants.” Nature Genetics 48(11):1418-1424 (2016)
Allele A
OR 1.32
p 1.0e-30
N 40,258
Large GWAS
European
Jin Y et al. “Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo.” The New England Journal of Medicine 362(18):1686-97 (2010)
Allele A
OR 1.38
p 2.0e-16
N 4,021
Large GWAS
European

autoimmune thyroid disease

Saevarsdottir S et al. “FLT3 stop mutation increases FLT3 ligand level and risk of autoimmune thyroid disease.” Nature 584(7822):619-623 (2020)
Allele A
OR 1.11
p 3.0e-30
N 754,406
Large GWAS
European
Zeng Y et al. “Genetic Associations Between Stress-Related Disorders and Autoimmune Disease.” The American Journal of Psychiatry 180(4):294-304 (2023)
Allele A
OR 1.10
p 3.0e-21
N 376,871
Large GWAS
European

Graves disease

White SL et al. “Global multi-ancestry genome-wide analyses identify genes and biological pathways associated with thyroid cancer and benign thyroid diseases.” Nature Genetics 58(2):307-316 (2026)
Allele A
OR 0.11
p 1.0e-13
N 2,460,657
Large GWAS
multi-ancestry

blood immunoglobulin amount

Wei Y et al. “Genome-wide association studies of thyroid-related hormones, dysfunction, and autoimmunity among 85,421 Chinese pregnancies.” Nature Communications 15(1):8004 (2024)
Allele C
OR 0.16
p 7.0e-15
N 60,225
Large GWAS
East Asian
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Research that mentions this SNP (2)

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Possible contribution of GSTP1 and other xenobiotic metabolizing genes to vitiligo susceptibility
AssociationN=200Mikhail M. Minashkin et al.(2013)· Archives of Dermatological Research

A candidate gene association study in 100 Russian vitiligo patients and 100 controls identified a strong novel association between GSTP1 rs1138272 (Ala114Val, OR=13.03, Bonferroni-adjusted P=0.0015) and vitiligo susceptibility. Cumulative analysis of multiple xenobiotic metabolizing genes showed that carrying higher numbers of risk alleles was associated with increased vitiligo risk (9-16 vs 3-8 alleles: OR=2.79, P=0.00063), supporting a polygenic model for vitiligo involving detoxification pathway genes.

Traits studied:Vitiligo
PubMedDOIMetascience Observatory
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Genome‐wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility
AssociationN=1,604Antonio Julià et al.(2008)· Arthritis &amp; Rheumatism

A two-stage genome-wide association study (GWAS) in Spanish population identified KLF12 as a new susceptibility locus for rheumatoid arthritis, with rs1324913 showing stronger association (P=0.01) in replication than PTPN22 rs2476601. Joint analysis with three previous GWAS studies confirmed KLF12 and PTPRT as commonly associated loci, with KLF12 SNP rs1887346 and rs9318228 showing P values of 6.03×10⁻⁵ and 3.66×10⁻⁵ in the discovery phase and evidence of replication across multiple populations.

Traits studied:Chronic inflammatory arthritisConnective tissue disordersCrohn's diseasePsoriatic arthritisRheumatoid arthritisSpondylarthritisSystemic lupus erythematosusType 1 diabetes mellitusVitiligo
PubMedDOIMetascience Observatory

About C1QTNF6

Enables identical protein binding activity. Predicted to be located in extracellular region and membrane. Predicted to be part of collagen trimer. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Jul 2025]

View all C1QTNF6 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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