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rs3819299

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(A;A) 0 common in clinvar
(A;C) 3 likely to carry one HLA-B27 allele, possible risk for B27 Syndromes.
(C;C) 3 likely to carry two HLA-B27 alleles, possible risk for B27 Syndromes.
ReferenceGRCh38 38.1/141
Chromosome6
Position31354590
GeneHLA-B
is asnp
is mentioned by
dbSNPrs3819299
dbSNP (classic)rs3819299
ClinGenrs3819299
ebirs3819299
HLIrs3819299
Exacrs3819299
Gnomadrs3819299
Varsomers3819299
LitVarrs3819299
Maprs3819299
PheGenIrs3819299
Biobankrs3819299
1000 genomesrs3819299
hgdprs3819299
ensemblrs3819299
geneviewrs3819299
scholarrs3819299
googlers3819299
pharmgkbrs3819299
gwascentralrs3819299
openSNPrs3819299
23andMers3819299
23andMe allrs3819299
SNPshotrs3819299
SNPdbers3819299
MSV3drs3819299
GWAS Ctlgrs3819299
GMAF0.107
Max Magnitude3

Perhaps the best known HLA-B27 tag SNP is rs116488202, located about 23kb away from rs3819299, but the former SNP is not tested on many platforms (for example, it is not tested by Ancestry), while the latter is and can be used as a proxy assuming strong enough linkage disequilibrium (which is likely at least in European populations but perhaps not others).

rs3819299 is reported to be associated with a (minor) impact on platelet count, but not with an association to ankylosing spondylitis (which is well reported as associated with HLA-B27).

rs3819299 is cited in this patent as associated with HLA-B*4002 in the JPT population

? (A;A) (A;C) (C;C) 28


ClinVar
Risk Rs3819299(C;C)
Alt Rs3819299(C;C)
Reference Rs3819299(A;A)
Significance Histocompatibility
Disease
Variation info
Gene HLA-B
CLNDBN
Reversed 1
HGVS NC_000006.11:g.31322367T>G
CLNSRC
CLNACC



GWAS snp
PMID [PMID 22139419OA-icon.png]
Trait Platelet counts
Title New gene functions in megakaryopoiesis and platelet formation.
Risk Allele G
P-val 9E-10
Odds Ratio 5.05 [3.43-6.66] 10^9/l increase