rs12060809

Homo sapiens
T>C
LCE2C : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0054 (1639/29974,GnomAD)
C=0085 (2490/29118,TOPMED)
C=0069 (348/5008,1000G)
C=0003 (12/3854,ALSPAC)
C=0002 (9/3708,TWINSUK)
chr1:152676474 (GRCh38.p7) (1q21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.152676474T>C
GRCh37.p13 chr 1NC_000001.10:g.152648950T>C

Gene: LCE2C, late cornified envelope 2C(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LCE2C transcriptNM_178429.3:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.749C=0.251
1000GenomesAmericanSub694T=0.990C=0.010
1000GenomesEast AsianSub1008T=1.000C=0.000
1000GenomesEuropeSub1006T=0.997C=0.003
1000GenomesGlobalStudy-wide5008T=0.931C=0.069
1000GenomesSouth AsianSub978T=0.990C=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.997C=0.003
The Genome Aggregation DatabaseAfricanSub8714T=0.817C=0.183
The Genome Aggregation DatabaseAmericanSub838T=0.990C=0.010
The Genome Aggregation DatabaseEast AsianSub1622T=1.000C=0.000
The Genome Aggregation DatabaseEuropeSub18498T=0.998C=0.001
The Genome Aggregation DatabaseGlobalStudy-wide29974T=0.945C=0.054
The Genome Aggregation DatabaseOtherSub302T=0.970C=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.914C=0.085
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.998C=0.002
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs120608090.00048alcohol dependence20201924

eQTL of rs12060809 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs12060809 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr1152652740152652839E0813790
chr1152653543152653753E0814593
chr1152654162152654454E0815212