rs4662641

Homo sapiens
G>A
LOC151121 : Non Coding Transcript Variant
LOC105373612 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0401 (12027/29922,GnomAD)
A=0359 (10478/29118,TOPMED)
A=0428 (2141/5008,1000G)
A=0455 (1755/3854,ALSPAC)
A=0470 (1744/3708,TWINSUK)
chr2:129242699 (GRCh38.p7) (2q21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
16 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.129242699G>A
GRCh37.p13 chr 2NC_000002.11:g.130000272G>A

Gene: LOC151121, uncharacterized LOC151121(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01854 transcript variant 2NR_122041.1:n.164...NR_122041.1:n.1642C>TC>TNon Coding Transcript Variant
LINC01854 transcript variant 1NR_122040.1:n.173...NR_122040.1:n.1730C>TC>TNon Coding Transcript Variant
LINC01854 transcript variant 3NR_122042.1:n.165...NR_122042.1:n.1653C>TC>TNon Coding Transcript Variant

Gene: LOC105373612, uncharacterized LOC105373612(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC105373612 transcriptXR_001739709.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.817A=0.183
1000GenomesAmericanSub694G=0.480A=0.520
1000GenomesEast AsianSub1008G=0.294A=0.706
1000GenomesEuropeSub1006G=0.568A=0.432
1000GenomesGlobalStudy-wide5008G=0.572A=0.428
1000GenomesSouth AsianSub978G=0.600A=0.400
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.545A=0.455
The Genome Aggregation DatabaseAfricanSub8712G=0.774A=0.226
The Genome Aggregation DatabaseAmericanSub838G=0.470A=0.530
The Genome Aggregation DatabaseEast AsianSub1620G=0.223A=0.777
The Genome Aggregation DatabaseEuropeSub18450G=0.553A=0.446
The Genome Aggregation DatabaseGlobalStudy-wide29922G=0.598A=0.401
The Genome Aggregation DatabaseOtherSub302G=0.620A=0.380
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.640A=0.359
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.530A=0.470
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
rs46626416.77E-06alcohol dependence (age at onset)24962325

eQTL of rs4662641 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 rs4662641 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 )
chr2129990903129991022E070-9250
chr2129991443129991904E070-8368
chr2129990903129991022E081-9250
chr2129991443129991904E081-8368
chr2129996773129997036E081-3236
chr2130010223130010353E0819951
chr2130010398130011293E08110126
chr2130038915130039052E08138643
chr2130039472130039687E08139200
chr2130039843130039996E08139571
chr2129996773129997036E082-3236
chr2130010223130010353E0829951
chr2130038591130038845E08238319
chr2130038915130039052E08238643
chr2130039472130039687E08239200
chr2130039843130039996E08239571