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rs12203592

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(C;C) 0 common on affy axiom data
(C;T) 2 Primarily in Europeans; slightly lighter hair and eye color, less tanning ability
(T;T) 2 Primarily in Europeans; slightly lighter hair and eye color, less tanning ability
ReferenceGRCh37 37.1/131
Chromosome6
Position396321
GeneIRF4
is asnp
is mentioned by
dbSNPrs12203592
ebirs12203592
HLIrs12203592
Exacrs12203592
Varsomers12203592
Maprs12203592
PheGenIrs12203592
hapmaprs12203592
1000 genomesrs12203592
hgdprs12203592
ensemblrs12203592
gopubmedrs12203592
geneviewrs12203592
scholarrs12203592
googlers12203592
pharmgkbrs12203592
gwascentralrs12203592
openSNPrs12203592
23andMers12203592
23andMe allrs12203592
SNP Nexus

SNPshotrs12203592
SNPdbers12203592
MSV3drs12203592
GWAS Ctlgrs12203592
GMAF0.05372
Max Magnitude2
? (C;C) (C;T) (T;T) 28

plos rs12203592 showed the largest allele frequency difference between the Irish individuals and those individuals of Northern, Central European and Eastern European descent

[PMID 18483556OA-icon.png] associated with hair color rs12896399 rs12203592

rs12203592 for freckling was previously associated with hair color, eye color, and tanning response to sunlight 10.1371/journal.pgen.1000993

10.1038/ncomms10815 A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features

GWAS
SNP rs12203592
PubMedID [PMID 18483556OA-icon.png]
Condition Black vs. red hair color
Gene IRF4
Risk Allele T
pValue 9.00E-028
OR 0.31
95% CI 0.25-0.36) decrease in hair color scor


[PMID 19396635OA-icon.png] Relationship between interferon regulatory factor 4 genetic polymorphisms, measures of sun sensitivity and risk for non-Hodgkin lymphoma


[PMID 19897031] An Intronic Polymorphism of IRF4 Gene Influences Gene Transcription in vitro and Shows a Risk Association with Childhood Acute Lymphoblastic Leukemia in Males



[PMID 20602913OA-icon.png] IRF4 Variants Have Age-Specific Effects on Nevus Count and Predispose to Melanoma

GWAS snp
PMID [PMID 20585627OA-icon.png]
Trait Eye color
Title Web-based, participant-driven studies yield novel genetic associations for common traits
Risk Allele T
P-val 2E-15
Odds Ratio 0.42 [NR] unit decrease


GWAS snp
PMID [PMID 21685912OA-icon.png]
Trait
Title Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy.
Risk Allele
P-val 6E-15
Odds Ratio 1.4800 [1.34-1.63]


[PMID 22512251] Potential association of single nucleotide polymorphisms in pigmentation genes with the development of basal cell carcinoma


[PMID 19340012OA-icon.png] Genome-wide association study of tanning phenotype in a population of European ancestry.


[PMID 19474294OA-icon.png] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.


[PMID 20018015OA-icon.png] Elastic-net regularization approaches for genome-wide association studies of rheumatoid arthritis.


[PMID 20463881OA-icon.png] Digital quantification of human eye color highlights genetic association of three new loci.


[PMID 21270109OA-icon.png] A germline variant in the interferon regulatory factor 4 gene as a novel skin cancer risk locus.


[PMID 21962134OA-icon.png] Polymorphisms in nevus-associated genes MTAP, PLA2G6, and IRF4 and the risk of invasive cutaneous melanoma.


GET Evidence
rs12203592
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.0859375
summary



Squamous Cell Carcinoma


[PMID 23393597OA-icon.png] Replication and Predictive Value of SNPs Associated with Melanoma and Pigmentation Traits in a Southern European Case-Control Study


[PMID 23537197OA-icon.png] Genetic variants in PARP1 (rs3219090) and IRF4 (rs12203592) genes associated with melanoma susceptibility in a Spanish population


[PMID 23548203OA-icon.png] Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans


[PMID 23771755OA-icon.png] Improved eye- and skin-color prediction based on 8 SNPs.


[PMID 24906573OA-icon.png] Association of interferon regulatory factor 4 gene polymorphisms rs12203592 and rs872071 with skin cancer and haematological malignancies susceptibility: a meta-analysis of 19 case-control studies


ClinVar
Risk rs12203592(T;T)
Alt rs12203592(T;T)
Reference rs12203592(C;C)
Significance Other
Disease Skin/hair/eye pigmentation
Variation info
Gene IRF4
CLNDBN Skin/hair/eye pigmentation, variation in, 8
Reversed 0
HGVS NC_000006.11:g.396321C>T
CLNSRC OMIM Allelic Variant
CLNACC RCV000148012.6,



[PMID 26857527] Association of Interferon Regulatory Factor-4 Polymorphism rs12203592 With Divergent Melanoma Pathways.


[PMID 27570521] Common Genetic Polymorphisms within NFκB-Related Genes and the Risk of Developing Invasive Aspergillosis.