rs699771

Homo sapiens
C>T
LOC105378934 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0059 (1774/29976,GnomAD)
T=0084 (2470/29118,TOPMED)
T=0113 (566/5008,1000G)
T=0008 (30/3854,ALSPAC)
T=0007 (27/3708,TWINSUK)
chr1:119329354 (GRCh38.p7) (1p12)
AD | ND
GWASdb2
4   publication(s)
See rs on genome
17 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.119329354C>T
GRCh37.p13 chr 1NC_000001.10:g.119871977C>T

Gene: LOC105378934, uncharacterized LOC105378934(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105378934 transcriptXR_947752.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.811T=0.189
1000GenomesAmericanSub694C=0.980T=0.020
1000GenomesEast AsianSub1008C=0.840T=0.160
1000GenomesEuropeSub1006C=0.985T=0.015
1000GenomesGlobalStudy-wide5008C=0.887T=0.113
1000GenomesSouth AsianSub978C=0.870T=0.130
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.992T=0.008
The Genome Aggregation DatabaseAfricanSub8714C=0.850T=0.150
The Genome Aggregation DatabaseAmericanSub836C=0.980T=0.020
The Genome Aggregation DatabaseEast AsianSub1620C=0.880T=0.120
The Genome Aggregation DatabaseEuropeSub18504C=0.986T=0.013
The Genome Aggregation DatabaseGlobalStudy-wide29976C=0.940T=0.059
The Genome Aggregation DatabaseOtherSub302C=0.980T=0.020
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.915T=0.084
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.993T=0.007
PMID Title Author Journal
22096494A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.Zuo LPLoS One
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology
20202923A genome-wide association study of alcohol dependence.Bierut LJProc Natl Acad Sci U S A
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs6997710.0000017alcohol dependence22096494
rs6997710.0000034alcohol and nictotine co-dependence22488850
rs6997710.00000887alcohol dependence20202923
rs6997710.000028alcohol dependence21956439

eQTL of rs699771 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 rs699771 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 )
chr1119868870119869562E070-2415
chr1119872303119872476E070326
chr1119872525119872715E070548
chr1119873739119873850E0701762
chr1119873922119873989E0701945
chr1119890560119890680E07018583
chr1119890743119890831E07018766
chr1119891029119891079E07019052
chr1119872303119872476E071326
chr1119903829119904359E07431852
chr1119904383119904433E07432406
chr1119844224119844284E081-27693
chr1119844691119844946E081-27031
chr1119846351119846404E081-25573
chr1119846466119846575E081-25402
chr1119846595119846751E081-25226
chr1119846770119846833E081-25144




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1119869604119870819E067-1158
chr1119869604119870819E068-1158
chr1119869604119870819E069-1158
chr1119869604119870819E070-1158
chr1119869604119870819E071-1158
chr1119869604119870819E072-1158
chr1119869604119870819E073-1158
chr1119869604119870819E074-1158
chr1119869604119870819E082-1158