rs1800012
| Orientation | minus |
| Stabilized | minus |
| 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 |
| Reference | GRCh38 38.1/141 |
| Chromosome | 17 |
| Position | 50200388 |
| Gene | COL1A1 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs1800012 |
| dbSNP (classic) | rs1800012 |
| ClinGen | rs1800012 |
| ebi | rs1800012 |
| HLI | rs1800012 |
| Exac | rs1800012 |
| Gnomad | rs1800012 |
| Varsome | rs1800012 |
| LitVar | rs1800012 |
| Map | rs1800012 |
| PheGenI | rs1800012 |
| Biobank | rs1800012 |
| 1000 genomes | rs1800012 |
| hgdp | rs1800012 |
| ensembl | rs1800012 |
| geneview | rs1800012 |
| scholar | rs1800012 |
| rs1800012 | |
| pharmgkb | rs1800012 |
| gwascentral | rs1800012 |
| openSNP | rs1800012 |
| 23andMe | rs1800012 |
| SNPshot | rs1800012 |
| SNPdbe | rs1800012 |
| MSV3d | rs1800012 |
| GWAS Ctlg | rs1800012 |
| GMAF | 0.1093 |
| Max Magnitude | 2 |
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 27917384
]:
- 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
[PMID 22174012] 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 15113403] 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 15157284] 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 17903296] 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 18787887] 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 19379518] Development of a fingerprinting panel using medically relevant polymorphisms.
[PMID 19841454] Collaborative meta-analysis: associations of 150 candidate genes with osteoporosis and osteoporotic fracture.
[PMID 20015871] Pharmacogenetic risk factors for altered bone mineral density and body composition in pediatric acute lymphoblastic leukemia.
[PMID 20798928] Polymorphisms in the 5' flank of COL1A1 gene and osteoporosis: meta-analysis of published studies.
[PMID 21269451] 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 28206959] Association of polymorphisms rs1800012 in COL1A1 with sports-related tendon and ligament injuries: a meta-analysis.
[PMID 29088884] Association of COL1A1 rs1800012 polymorphism with musculoskeletal degenerative diseases: a meta-analysis.
[PMID 29799806] Variations of Collagen-Encoding Genes are Associated with Exercise-Induced Muscle Damage.
