rs16891982
| hair colour, melanoma |
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 1.1 | generally non-European, but if European, 7x more likely to have black hair |
| (C;G) | 2 | if European, 7x more likely to have black hair |
| (G;G) | 1.1 | Generally European; Light skin; Possibly an increased risk of melanoma |
| Reference | GRCh38 38.1/141 |
| Chromosome | 5 |
| Position | 33951588 |
| Gene | SLC45A2 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs16891982 |
| dbSNP (classic) | rs16891982 |
| ClinGen | rs16891982 |
| ebi | rs16891982 |
| HLI | rs16891982 |
| Exac | rs16891982 |
| Gnomad | rs16891982 |
| Varsome | rs16891982 |
| LitVar | rs16891982 |
| Map | rs16891982 |
| PheGenI | rs16891982 |
| Biobank | rs16891982 |
| 1000 genomes | rs16891982 |
| hgdp | rs16891982 |
| ensembl | rs16891982 |
| geneview | rs16891982 |
| scholar | rs16891982 |
| rs16891982 | |
| pharmgkb | rs16891982 |
| gwascentral | rs16891982 |
| openSNP | rs16891982 |
| 23andMe | rs16891982 |
| SNPshot | rs16891982 |
| SNPdbe | rs16891982 |
| MSV3d | rs16891982 |
| GWAS Ctlg | rs16891982 |
| Merged from | Rs17855902 |
| GMAF | 0.4408 |
| Max Magnitude | 2 |
| ? | (C;C) (C;G) (G;G) | 28 |
|---|---|---|
|
| ||
This snp influences skin pigmentation. The allele p.L374F indicates light-skinned european ancestry [PMID 16847698]
[PMID 18563784] c.1122C>G, p.Phe374Leu (NCBI dbSNP rs16891982) in SLC45A2 was associated with protection from malignant melanoma (OR, 0.41; 95% CI, 0.24-0.70; P=0.008 after adjustment for multiple testing)
An association study conducted on a population of European origin concluded that the rare (in Europeans, at least) allele L374, i.e. rs16891982(C) in dbSNP orientation, significantly increases the possibility of having black hair color, with an odds ratio of around 7.[PMID 18806926]
| GWAS | |
|---|---|
| SNP | rs16891982 |
| PubMedID | [PMID 17999355 ]
|
| Condition | Skin pigmentation by reflectance spectroscopy |
| Gene | SLC45A2 |
| Risk Allele | C |
| pValue | 3.00E-011 |
| OR | 4.86 |
| 95% CI | 2.88-8.21 |
[PMID 19710684] This population-based case-control study investigated a number of pigmentation-related SNPs and their correlation with cutaneous malignant melanoma (CMM) in an Australian population. rs16891982 (variant F374L) was found to be associated with odds ratios of 3.44, 2.86, 1.68, and 1.68 for all study subjects (1,738 CMM cases and 4,517 controls), subjects with northern European ancestry (1,438 cases and 3,098 controls), northern European subjects adjusted for hair, eye, and skin colour, and northern European subjects adjusted for the MC1R genotype, respectively (p<0.001 for all).
| GWAS snp | |
|---|---|
| PMID | [PMID 20585627]
|
| Trait | Eye color |
| Title | Web-based, participant-driven studies yield novel genetic associations for common traits |
| Risk Allele | C |
| P-val | 1E-12 |
| Odds Ratio | 0.84 [NR] unit increase |
[PMID 20457063] Human eye colour and HERC2, OCA2 and MATP
| ClinVar | |
|---|---|
| Risk | Rs16891982(G;G) |
| Alt | Rs16891982(G;G) |
| Reference | Rs16891982(C;C) |
| Significance | Other |
| Disease | Skin/hair/eye pigmentation Malignant melanoma of skin not specified |
| Variation | info |
| Gene | SLC45A2 |
| CLNDBN | Skin/hair/eye pigmentation, variation in, 5 Malignant melanoma of skin not specified |
| Reversed | 0 |
| HGVS | NC_000005.9:g.33951693C\x3d; NC_000005.9:g.33951693C>G |
| CLNSRC | OMIM Allelic Variant |
| CLNACC | RCV000004763.4, RCV000022392.1, RCV000178963.1, |
[PMID 18483556] A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation.
[PMID 19340012] Genome-wide association study of tanning phenotype in a population of European ancestry.
[PMID 19384953] Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians.
[PMID 19440451] Haplotypes in SLC24A5 Gene as Ancestry Informative Markers in Different Populations.
[PMID 19668368] Ancestry analysis in the 11-M Madrid bomb attack investigation.
[PMID 20042077] Genetic determinants of hair and eye colours in the Scottish and Danish populations.
[PMID 20463881] Digital quantification of human eye color highlights genetic association of three new loci.
[PMID 20806075] Spectrum of candidate gene mutations associated with Indian familial oculocutaneous and ocular albinism.
[PMID 20850402] Genetic analysis of the SNPforID 34-plex ancestry informative SNP panel in Tunisian and Libyan populations.
[PMID 22912732] Skin Color Variation in Orang Asli Tribes of Peninsular Malaysia
[PMID 23100201] A single-nucleotide polymorphism (SNP) multiplex system: the association of five SNPs with human eye and hair color in the Slovenian population and comparison using a Bayesian network and logistic regression model
[PMID 23393597] Replication and Predictive Value of SNPs Associated with Melanoma and Pigmentation Traits in a Southern European Case-Control Study
[PMID 23786662] Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS)
[PMID 23771755] Improved eye- and skin-color prediction based on 8 SNPs.
[PMID 25093503] The Interplay between Natural Selection and Susceptibility to Melanoma on Allele 374F of SLC45A2 Gene in a South European Population
[PMID 25142205] Assessment of high resolution melting analysis as a potential SNP genotyping technique in forensic casework
[PMID 28242083] Association of five SNPs with human hair colour in the Polish population.
[PMID 33167923] Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil.
