rs42041

This is a intron variant variant in the CDK6 gene.

GWAS Catalog Trait Associations (3)

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

body height

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 C
OR 0.10
p 1.0e-118
N 607,511
Major Consortium StudyLarge GWAS
multi-ancestry
Allele C
OR 0.05
p 7.0e-32
N 293,593
Large GWAS
African unspecified

BMI-adjusted hip circumference

Allele G
OR 0.05
p 4.0e-37
N 186,825
Major Consortium StudyLarge GWAS
European

eosinophil count

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 C
OR 0.02
p 4.0e-14
N 485,659
Major Consortium StudyLarge GWAS
multi-ancestry

Research that mentions this SNP (3)

Rheumatoid arthritis risk allele PTPRC is also associated with response to anti–tumor necrosis factor α therapy
AssociationN=1,283Cui J. et al.(2010)· Arthritis &amp; Rheumatism

This multi-cohort genetic association study of 1,283 RA patients found that the PTPRC/CD45 gene variant rs10919563 (G allele) is associated with favorable response to anti-TNF therapy (OR 0.55, P=0.0001). Of 31 established RA risk alleles tested, only PTPRC reached genome-wide significance for therapy response, with stronger associations in autoantibody-positive patients (OR 0.55, 95% CI 0.39-0.76) compared to seronegative patients.

Traits studied:Response to anti-TNF therapyRheumatoid Arthritis
A functionally relevant IRF5 haplotype is associated with reduced risk to Wegener’s granulomatosis
AssociationN=1,616Stefan Wieczorek et al.(2010)· Journal of Molecular Medicine

This association study of 664 German Wegener's granulomatosis (WG) patients and 952 controls evaluated 22 SNPs across 13 candidate genes identified from RA and SLE studies. The strongest finding was a protective four-SNP IRF5 haplotype (rs2004640_G/rs60344245_del/rs2070197_T/rs10954213_G) with reduced WG risk (p=0.0000897, OR 0.73, 95% CI 0.62-0.85). SNPs in TNFAIP3 and CDK6 also showed nominally significant associations, suggesting WG shares some genetic risk factors with other autoimmune diseases.

Traits studied:Granulomatous inflammationRheumatoid arthritisSjögren's syndromeSystemic lupus erythematosusSystemic sclerosisSystemic vasculitisType 1 diabetesWegener's granulomatosis
Association of a single‐nucleotide polymorphism in CD40 with the rate of joint destruction in rheumatoid arthritis
AssociationN=956Michael P. M. van der Linden et al.(2009)· Arthritis &amp; Rheumatism

This association study examined whether six genetic variants identified in RA susceptibility studies also influence radiographic joint destruction severity. In ACPA-positive RA patients, rs4810485 in CD40 showed significant association with increased radiographic progression rate (1.12x greater annual Sharp score increase per risk allele, P=0.003), which was independently replicated in the NARAC cohort (P=0.021). This represents the first non-HLA-related genetic severity factor for RA progression that has been replicated across independent cohorts.

Traits studied:Joint destruction severityRadiographic progression in ACPA-positive RARheumatoid arthritis

About CDK6

The protein encoded by this gene is a member of the CMGC family of serine/threonine protein kinases. This kinase is a catalytic subunit of the protein kinase complex that is important for cell cycle G1 phase progression and G1/S transition. The activity of this kinase first appears in mid-G1 phase, which is controlled by the regulatory subunits including D-type cyclins and members of INK4 family of CDK inhibitors. This kinase, as well as CDK4, has been shown to phosphorylate, and thus regulate the activity of, tumor suppressor protein Rb. Altered expression of this gene has been observed in multiple human cancers. A mutation in this gene resulting in reduced cell proliferation, and impaired cell motility and polarity, and has been identified in patients with primary microcephaly. [provided by RefSeq, Aug 2017]

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Gene information from NCBI Gene. Variant classifications from ClinVar.

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