rs4662640

Homo sapiens
A>C
LOC151121 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0402 (12049/29912,GnomAD)
C=0359 (10479/29118,TOPMED)
C=0428 (2141/5008,1000G)
C=0455 (1755/3854,ALSPAC)
C=0471 (1745/3708,TWINSUK)
chr2:129242223 (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.129242223A>C
GRCh37.p13 chr 2NC_000002.11:g.129999796A>C

Gene: LOC151121, uncharacterized LOC151121(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01854 transcript variant 2NR_122041.1:n.211...NR_122041.1:n.2118T>GT>GNon Coding Transcript Variant
LINC01854 transcript variant 1NR_122040.1:n.220...NR_122040.1:n.2206T>GT>GNon Coding Transcript Variant
LINC01854 transcript variant 3NR_122042.1:n.212...NR_122042.1:n.2129T>GT>GNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.817C=0.183
1000GenomesAmericanSub694A=0.480C=0.520
1000GenomesEast AsianSub1008A=0.294C=0.706
1000GenomesEuropeSub1006A=0.568C=0.432
1000GenomesGlobalStudy-wide5008A=0.572C=0.428
1000GenomesSouth AsianSub978A=0.600C=0.400
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.545C=0.455
The Genome Aggregation DatabaseAfricanSub8694A=0.773C=0.227
The Genome Aggregation DatabaseAmericanSub838A=0.470C=0.530
The Genome Aggregation DatabaseEast AsianSub1614A=0.224C=0.776
The Genome Aggregation DatabaseEuropeSub18464A=0.552C=0.447
The Genome Aggregation DatabaseGlobalStudy-wide29912A=0.597C=0.402
The Genome Aggregation DatabaseOtherSub302A=0.620C=0.380
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.640C=0.359
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.529C=0.471
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
rs46626406.77E-06alcohol dependence (age at onset)24962325

eQTL of rs4662640 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 rs4662640 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 )
chr2129990903129991022E070-8774
chr2129991443129991904E070-7892
chr2129990903129991022E081-8774
chr2129991443129991904E081-7892
chr2129996773129997036E081-2760
chr2130010223130010353E08110427
chr2130010398130011293E08110602
chr2130038915130039052E08139119
chr2130039472130039687E08139676
chr2130039843130039996E08140047
chr2129996773129997036E082-2760
chr2130010223130010353E08210427
chr2130038591130038845E08238795
chr2130038915130039052E08239119
chr2130039472130039687E08239676
chr2130039843130039996E08240047