rs17769849

Homo sapiens
C>T
LOC105377564 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0321 (9616/29902,GnomAD)
T=0248 (7240/29118,TOPMED)
T=0272 (1360/5008,1000G)
T=0375 (1447/3854,ALSPAC)
T=0392 (1454/3708,TWINSUK)
chr4:179978312 (GRCh38.p7) (4q34.3)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.179978312C>T
GRCh37.p13 chr 4NC_000004.11:g.180899465C>T

Gene: LOC105377564, uncharacterized LOC105377564(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377564 transcript variant X2XR_001741480.1:n.N/AIntron Variant
LOC105377564 transcript variant X1XR_939516.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.883T=0.117
1000GenomesAmericanSub694C=0.710T=0.290
1000GenomesEast AsianSub1008C=0.673T=0.327
1000GenomesEuropeSub1006C=0.647T=0.353
1000GenomesGlobalStudy-wide5008C=0.728T=0.272
1000GenomesSouth AsianSub978C=0.670T=0.330
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.625T=0.375
The Genome Aggregation DatabaseAfricanSub8714C=0.846T=0.154
The Genome Aggregation DatabaseAmericanSub836C=0.660T=0.340
The Genome Aggregation DatabaseEast AsianSub1614C=0.660T=0.340
The Genome Aggregation DatabaseEuropeSub18436C=0.600T=0.399
The Genome Aggregation DatabaseGlobalStudy-wide29902C=0.678T=0.321
The Genome Aggregation DatabaseOtherSub302C=0.770T=0.230
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.751T=0.248
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.608T=0.392
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs177698490.00054alcohol dependence20201924

eQTL of rs17769849 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 rs17769849 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.