rs1934990

Homo sapiens
C>A
LOC107986640 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0041 (1248/29974,GnomAD)
A=0049 (1437/29118,TOPMED)
A=0024 (118/5008,1000G)
A=0070 (270/3854,ALSPAC)
A=0063 (235/3708,TWINSUK)
chr6:125345675 (GRCh38.p7) (6q22.31)
AD
GWASdb2
1   publication(s)
See rs on genome
59 Enhancers around
34 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.125345675C>A
GRCh37.p13 chr 6NC_000006.11:g.125666821C>A

Gene: LOC107986640, uncharacterized LOC107986640(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC107986640 transcript variant X1XR_001744327.1:n.N/AUpstream Transcript Variant
LOC107986640 transcript variant X2XR_001744328.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.998A=0.002
1000GenomesAmericanSub694C=0.940A=0.060
1000GenomesEast AsianSub1008C=0.999A=0.001
1000GenomesEuropeSub1006C=0.936A=0.064
1000GenomesGlobalStudy-wide5008C=0.976A=0.024
1000GenomesSouth AsianSub978C=0.990A=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.930A=0.070
The Genome Aggregation DatabaseAfricanSub8728C=0.988A=0.012
The Genome Aggregation DatabaseAmericanSub838C=0.960A=0.040
The Genome Aggregation DatabaseEast AsianSub1620C=0.999A=0.001
The Genome Aggregation DatabaseEuropeSub18486C=0.941A=0.058
The Genome Aggregation DatabaseGlobalStudy-wide29974C=0.958A=0.041
The Genome Aggregation DatabaseOtherSub302C=0.930A=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.950A=0.049
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.937A=0.063
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs19349906.54E-05alcohol dependence21703634

eQTL of rs1934990 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:125666821HDDC2ENSG00000111906.13C>A3.6028e-943539Cortex

meQTL of rs1934990 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 )
chr6125621245125621333E067-45488
chr6125632159125632663E067-34158
chr6125635192125635750E067-31071
chr6125635930125636010E067-30811
chr6125678414125678484E06711593
chr6125678521125679255E06711700
chr6125679308125679388E06712487
chr6125683672125684121E06716851
chr6125617521125617698E068-49123
chr6125617748125617920E068-48901
chr6125621245125621333E068-45488
chr6125632159125632663E068-34158
chr6125648230125648280E068-18541
chr6125678137125678323E06811316
chr6125678414125678484E06811593
chr6125678521125679255E06811700
chr6125679308125679388E06812487
chr6125619676125619771E069-47050
chr6125620505125620821E069-46000
chr6125621245125621333E069-45488
chr6125632159125632663E069-34158
chr6125635192125635750E069-31071
chr6125678414125678484E06911593
chr6125678521125679255E06911700
chr6125679308125679388E06912487
chr6125617521125617698E070-49123
chr6125617748125617920E070-48901
chr6125618027125618728E070-48093
chr6125667173125668030E070352
chr6125678137125678323E07011316
chr6125678414125678484E07011593
chr6125678521125679255E07011700
chr6125679308125679388E07012487
chr6125617521125617698E071-49123
chr6125621245125621333E071-45488
chr6125632159125632663E071-34158
chr6125678137125678323E07111316
chr6125678414125678484E07111593
chr6125678521125679255E07111700
chr6125679308125679388E07112487
chr6125680037125680353E07113216
chr6125632159125632663E072-34158
chr6125678137125678323E07211316
chr6125678414125678484E07211593
chr6125678521125679255E07211700
chr6125679308125679388E07212487
chr6125621245125621333E073-45488
chr6125632159125632663E073-34158
chr6125678137125678323E07311316
chr6125678414125678484E07311593
chr6125678521125679255E07311700
chr6125632159125632663E074-34158
chr6125678137125678323E07411316
chr6125678414125678484E07411593
chr6125678521125679255E07411700
chr6125678137125678323E08111316
chr6125678414125678484E08111593
chr6125678521125679255E08111700
chr6125678521125679255E08211700










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr6125621966125622026E067-44795
chr6125622058125623693E067-43128
chr6125637713125638134E067-28687
chr6125684168125685307E06717347
chr6125621966125622026E068-44795
chr6125622058125623693E068-43128
chr6125637713125638134E068-28687
chr6125684168125685307E06817347
chr6125621966125622026E069-44795
chr6125622058125623693E069-43128
chr6125637713125638134E069-28687
chr6125684168125685307E06917347
chr6125621966125622026E070-44795
chr6125622058125623693E070-43128
chr6125621966125622026E071-44795
chr6125622058125623693E071-43128
chr6125637713125638134E071-28687
chr6125684168125685307E07117347
chr6125621966125622026E072-44795
chr6125622058125623693E072-43128
chr6125637713125638134E072-28687
chr6125684168125685307E07217347
chr6125621966125622026E073-44795
chr6125622058125623693E073-43128
chr6125684168125685307E07317347
chr6125621966125622026E074-44795
chr6125622058125623693E074-43128
chr6125637713125638134E074-28687
chr6125684168125685307E07417347
chr6125621966125622026E081-44795
chr6125622058125623693E081-43128
chr6125621966125622026E082-44795
chr6125622058125623693E082-43128
chr6125684168125685307E08217347