rs7909889

Homo sapiens
C>T
LOC105378314 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0195 (5846/29890,GnomAD)
T=0233 (6809/29118,TOPMED)
T=0162 (809/5008,1000G)
T=0183 (707/3854,ALSPAC)
T=0177 (657/3708,TWINSUK)
chr10:57812610 (GRCh38.p7) (10q21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
10 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.57812610C>T
GRCh37.p13 chr 10NC_000010.10:g.59572370C>T

Gene: LOC105378314, uncharacterized LOC105378314(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105378314 transcriptXR_001747454.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.673T=0.327
1000GenomesAmericanSub694C=0.870T=0.130
1000GenomesEast AsianSub1008C=0.999T=0.001
1000GenomesEuropeSub1006C=0.807T=0.193
1000GenomesGlobalStudy-wide5008C=0.838T=0.162
1000GenomesSouth AsianSub978C=0.900T=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.817T=0.183
The Genome Aggregation DatabaseAfricanSub8708C=0.701T=0.299
The Genome Aggregation DatabaseAmericanSub834C=0.870T=0.130
The Genome Aggregation DatabaseEast AsianSub1606C=0.999T=0.001
The Genome Aggregation DatabaseEuropeSub18442C=0.834T=0.166
The Genome Aggregation DatabaseGlobalStudy-wide29890C=0.804T=0.195
The Genome Aggregation DatabaseOtherSub300C=0.780T=0.220
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.766T=0.233
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.823T=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
rs79098893.29E-06alcohol dependence (age at onset)24962325

eQTL of rs7909889 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 rs7909889 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 )
chr105954655759547364E070-25006
chr105954790159548037E070-24333
chr105954805259548139E070-24231
chr105960769459607836E07035324
chr105960799559608117E07035625
chr105960825459608428E07035884
chr105960867459608744E07036304
chr105960879059608912E07036420
chr105960943659609587E07037066
chr105960963359609777E07037263