rs17625002

Homo sapiens
T>G
LOC105378314 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0117 (3505/29870,GnomAD)
G=0110 (3208/29118,TOPMED)
G=0076 (379/5008,1000G)
G=0183 (707/3854,ALSPAC)
G=0178 (660/3708,TWINSUK)
chr10:57799360 (GRCh38.p7) (10q21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
8 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.57799360T>G
GRCh37.p13 chr 10NC_000010.10:g.59559120T>G

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
1000GenomesAfricanSub1322T=0.984G=0.016
1000GenomesAmericanSub694T=0.900G=0.100
1000GenomesEast AsianSub1008T=0.999G=0.001
1000GenomesEuropeSub1006T=0.807G=0.193
1000GenomesGlobalStudy-wide5008T=0.924G=0.076
1000GenomesSouth AsianSub978T=0.900G=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.817G=0.183
The Genome Aggregation DatabaseAfricanSub8720T=0.965G=0.035
The Genome Aggregation DatabaseAmericanSub838T=0.890G=0.110
The Genome Aggregation DatabaseEast AsianSub1586T=0.999G=0.001
The Genome Aggregation DatabaseEuropeSub18424T=0.834G=0.165
The Genome Aggregation DatabaseGlobalStudy-wide29870T=0.882G=0.117
The Genome Aggregation DatabaseOtherSub302T=0.780G=0.220
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.889G=0.110
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.822G=0.178
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
rs176250023.93E-06alcohol dependence (age at onset)24962325

eQTL of rs17625002 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 rs17625002 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 )
chr105954655759547364E070-11756
chr105954790159548037E070-11083
chr105954805259548139E070-10981
chr105960769459607836E07048574
chr105960799559608117E07048875
chr105960825459608428E07049134
chr105960867459608744E07049554
chr105960879059608912E07049670