rs17078679

Homo sapiens
A>G
LOC105370290 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0097 (2916/29818,GnomAD)
G=0094 (2764/29118,TOPMED)
G=0113 (564/5008,1000G)
G=0066 (255/3854,ALSPAC)
G=0062 (231/3708,TWINSUK)
chr13:84882257 (GRCh38.p7) (13q31.1)
AD
GWASdb2
1   publication(s)
See rs on genome
2 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.84882257A>G
GRCh37.p13 chr 13NC_000013.10:g.85456392A>G

Gene: LOC105370290, uncharacterized LOC105370290(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105370290 transcript variant X2XR_001749949.1:n.N/AIntron Variant
LOC105370290 transcript variant X1XR_942135.1:n.N/AIntron Variant
LOC105370290 transcript variant X4XR_942136.1:n.N/AIntron Variant
LOC105370290 transcript variant X3XR_942137.1:n.N/AIntron Variant
LOC105370290 transcript variant X5XR_942138.2:n.N/AIntron Variant
LOC105370290 transcript variant X6XR_942139.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.845G=0.155
1000GenomesAmericanSub694A=0.820G=0.180
1000GenomesEast AsianSub1008A=0.897G=0.103
1000GenomesEuropeSub1006A=0.925G=0.075
1000GenomesGlobalStudy-wide5008A=0.887G=0.113
1000GenomesSouth AsianSub978A=0.940G=0.060
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.934G=0.066
The Genome Aggregation DatabaseAfricanSub8682A=0.865G=0.135
The Genome Aggregation DatabaseAmericanSub834A=0.840G=0.160
The Genome Aggregation DatabaseEast AsianSub1622A=0.922G=0.078
The Genome Aggregation DatabaseEuropeSub18378A=0.919G=0.080
The Genome Aggregation DatabaseGlobalStudy-wide29818A=0.902G=0.097
The Genome Aggregation DatabaseOtherSub302A=0.960G=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.905G=0.094
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.938G=0.062
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
rs170786790.00041alcohol dependence20201924

eQTL of rs17078679 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 rs17078679 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 )
chr138543989785440476E071-15916
chr138543989785440476E072-15916