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rs747650

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(A;A) Low risk of acne occurences in Chinese Han population
(A;G) Higher risk of acne occurrences in Chinese Han population
(G;G) Higher risk of acne occurences in Chinese Han Population
ReferenceGRCh38 38.1/142
Chromosome11
Position47154454
GeneC11orf49
is asnp
is mentioned by
dbSNPrs747650
ebirs747650
HLIrs747650
Exacrs747650
Varsomers747650
Maprs747650
PheGenIrs747650
hapmaprs747650
1000 genomesrs747650
hgdprs747650
ensemblrs747650
gopubmedrs747650
geneviewrs747650
scholarrs747650
googlers747650
pharmgkbrs747650
gwascentralrs747650
openSNPrs747650
23andMers747650
23andMe allrs747650
SNP Nexus

SNPshotrs747650
SNPdbers747650
MSV3drs747650
GWAS Ctlgrs747650
Max Magnitude
? (A;A) (A;G) (G;G) 28
GWAS snp
PMID [PMID 24399259]
Trait Acne (severe)
Title Two new susceptibility loci 1q24.2 and 11p11.2 confer risk to severe acne.
Risk Allele G
P-val 4E-9
Odds Ratio 1.24 [1.16-1.34]

rs747650 is a variant on chromosome 11p11.2 associated with acne. rs747650-G (reference major allele A, + strand) was identified as a risk allele associated with severe acne in a two-stage genome-wide association study with Han Chinese individuals by He et al. (PMID 24399259). An initial GWAS (1031 cases of severe acne and 1031 selected control subjects without acne) identified 101 SNPs with evidence of association (P<1x10^-4 or P<1x10^-2 located within/near nine candidate susceptibility genes) including rs747650 (p = 8.12x10^-5, OR 95% CI 1.14-1.47). These SNPs were further evaluated in an independent cohort (1860 cases and 3660 controls). The replication round identified 3 SNPs achieving genome-wide significance including rs747650 (p = 9.25x10^-6, OR 95% CI 1.12-1.33) with an overall combined P=4.41x10^-9 / OR 95% CI 1.16-1.34. No significant association for this SNP was found in a similar study in European individuals from the United Kingdom which was sufficiently powered for the reported effect size in the Han Chinese study.

rs747650 is the lead SNP and is located within an intron of C11ORF49. It is unknown whether this variant has any causal influence on severe acne. One hypothesis is that rs747650 may be an eQTL involved in transcriptional regulation, based on ENCODE data indicating a peak density of DNAse hypersensitivity, histone marks and transcription factor ChIP overlapping this locus. He et al. speculates that a neighboring gene DDB2 is a potential candidate gene for acne susceptibility based on its implication in androgen metabolism and inflammation.

References:

[PMID 24399259]