rs11840139

Homo sapiens
T>C
LOC105370217 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0158 (4719/29870,GnomAD)
C=0139 (4056/29116,TOPMED)
C=0137 (686/5008,1000G)
C=0161 (621/3854,ALSPAC)
C=0177 (657/3708,TWINSUK)
chr13:57480807 (GRCh38.p7) (13q21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
2 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.57480807T>C
GRCh37.p13 chr 13NC_000013.10:g.58054941T>C

Gene: LOC105370217, uncharacterized LOC105370217(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105370217 transcriptXR_941983.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.884C=0.116
1000GenomesAmericanSub694T=0.930C=0.070
1000GenomesEast AsianSub1008T=0.789C=0.211
1000GenomesEuropeSub1006T=0.832C=0.168
1000GenomesGlobalStudy-wide5008T=0.863C=0.137
1000GenomesSouth AsianSub978T=0.900C=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.839C=0.161
The Genome Aggregation DatabaseAfricanSub8726T=0.892C=0.108
The Genome Aggregation DatabaseAmericanSub834T=0.920C=0.080
The Genome Aggregation DatabaseEast AsianSub1570T=0.790C=0.210
The Genome Aggregation DatabaseEuropeSub18438T=0.818C=0.181
The Genome Aggregation DatabaseGlobalStudy-wide29870T=0.842C=0.158
The Genome Aggregation DatabaseOtherSub302T=0.860C=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.860C=0.139
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.823C=0.177
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs118401395.47E-06alcohol dependence (age at onset)24962325

eQTL of rs11840139 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 rs11840139 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 )
chr135802517758025303E081-29638
chr135806669158066859E08111750