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rs1800012

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(G;G) 0 normal
(G;T) normal
(T;T) 2 Complex; possibly lower risk of ACL ruptures, yet higher risk for bone loss and disc disease
ReferenceGRCh38 38.1/141
Chromosome17
Position50200388
GeneCOL1A1
is asnp
is mentioned by
dbSNPrs1800012
dbSNP (classic)rs1800012
ClinGenrs1800012
ebirs1800012
HLIrs1800012
Exacrs1800012
Gnomadrs1800012
Varsomers1800012
LitVarrs1800012
Maprs1800012
PheGenIrs1800012
Biobankrs1800012
1000 genomesrs1800012
hgdprs1800012
ensemblrs1800012
geneviewrs1800012
scholarrs1800012
googlers1800012
pharmgkbrs1800012
gwascentralrs1800012
openSNPrs1800012
23andMers1800012
23andMe allrs1800012
SNPshotrs1800012
SNPdbers1800012
MSV3drs1800012
GWAS Ctlgrs1800012
GMAF0.1093
Max Magnitude2

rs1800012 represents a common (allele frequency ~20%) polymorphism consisting of a G-to-T substitution at the first base of a consensus site for the transcription factor Sp1 in the first intron of the COL1A1 gene. The rs1800012(T) allele has been extensively studied, with most observations supporting at least some association with decreased bone mineral density, and increased risk for osteoporosis, fractures, and intervertebral disc disease.

[PMID 19193663] rs1800012(T;T) was significantly (p=0.031, OR=0.08, 95%CI <0.01 to 1.46) under-represented in South African participants with anterior cruciate ligament ruptures, based on a study of ~100 patients vs ~100 controls.

Summary relevant to intervertebral disc disease for rs1800012(T), from [PMID 27917384OA-icon.png]:

  • odds ratio (OR) 3.6 for TT genotype compared with GT or GG, in study of 966 elderly Dutch
  • T allele associated with more severe IVDD in study of 75 Southern European male patients vs 25 controls
OMIM120150
DescCOLLAGEN, TYPE I, ALPHA-1; COL1A1
Variant
Relatedalso
OMIM120150
Desc
Variant0051
Relatedalso
OMIM166710
Desc
Variant
Relatedalso


[PMID 22174012OA-icon.png] JAG1 and COL1A1 polymorphisms and haplotypes in relation to bone mineral density variations in postmenopausal Mexican-Mestizo Women


[PMID 22190259] COL1A1 haplotypes and hip fracture


[PMID 15113403OA-icon.png] Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis.


[PMID 15157284OA-icon.png] Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes.


[PMID 16804049] Haplotypes defined by promoter and intron 1 polymorphisms of the COLIA1 gene regulate bone mineral density in women.


[PMID 17303000] Association and linkage analysis of COL1A1 and AHSG gene polymorphisms with femoral neck bone geometric parameters in both Caucasian and Chinese nuclear families.


[PMID 17903296OA-icon.png] Genome-wide association with bone mass and geometry in the Framingham Heart Study.


[PMID 18353721] Investigation of the Sp1-binding site polymorphism within the COL1A1 gene in participants with Achilles tendon injuries and controls.


[PMID 18787887OA-icon.png] Genetic variation in candidate osteoporosis genes, bone mineral density, and fracture risk: the study of osteoporotic fractures.


[PMID 19016596] A rare haplotype in the upstream regulatory region of COL1A1 is associated with reduced bone quality and hip fracture.


[PMID 19379518OA-icon.png] Development of a fingerprinting panel using medically relevant polymorphisms.


[PMID 19841454OA-icon.png] Collaborative meta-analysis: associations of 150 candidate genes with osteoporosis and osteoporotic fracture.


[PMID 20015871OA-icon.png] Pharmacogenetic risk factors for altered bone mineral density and body composition in pediatric acute lymphoblastic leukemia.


[PMID 20798928OA-icon.png] Polymorphisms in the 5' flank of COL1A1 gene and osteoporosis: meta-analysis of published studies.


[PMID 21269451OA-icon.png] Synopsis and meta-analysis of genetic association studies in osteoporosis for the focal adhesion family genes: the CUMAGAS-OSTEOporosis information system.


[PMID 21396799] Genetic polymorphisms and other risk factors associated with bisphosphonate induced osteonecrosis of the jaw.


[PMID 22057139] A haplotype derived from the common variants at the -1997G/T and Sp1 binding site of the COL1A1 gene influences risk of postmenopausal osteoporosis in India.


[PMID 22066665] Bone mineral density and genetic markers involved in three connected pathways (focal adhesion, actin cytoskeleton regulation and cell cycle): the CUMAGAS-BMD information system.


ClinVar
Risk Rs1800012(T;T)
Alt Rs1800012(T;T)
Reference Rs1800012(G;G)
Significance Other
Disease Bone mineral density variation quantitative trait locus
Variation info
Gene COL1A1
CLNDBN Bone mineral density variation quantitative trait locus
Reversed 1
HGVS NC_000017.10:g.48277749C\x3d
CLNSRC OMIM Allelic Variant
CLNACC RCV000018874.2,



[PMID 28206959OA-icon.png] Association of polymorphisms rs1800012 in COL1A1 with sports-related tendon and ligament injuries: a meta-analysis.


[PMID 29088884OA-icon.png] Association of COL1A1 rs1800012 polymorphism with musculoskeletal degenerative diseases: a meta-analysis.


[PMID 29799806OA-icon.png] Variations of Collagen-Encoding Genes are Associated with Exercise-Induced Muscle Damage.