rs10847023

Homo sapiens
T>C
LINC00939 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0144 (4328/29956,GnomAD)
C=0144 (4195/29118,TOPMED)
C=0145 (725/5008,1000G)
C=0159 (614/3854,ALSPAC)
C=0170 (631/3708,TWINSUK)
chr12:125959974 (GRCh38.p7) (12q24.32)
AD
GWASdb2
1   publication(s)
See rs on genome
10 Enhancers around
14 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.125959974T>C
GRCh37.p13 chr 12NC_000012.11:g.126444520T>C

Gene: LINC00939, long intergenic non-protein coding RNA 939(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00939 transcriptNR_034132.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.897C=0.103
1000GenomesAmericanSub694T=0.620C=0.380
1000GenomesEast AsianSub1008T=0.969C=0.031
1000GenomesEuropeSub1006T=0.836C=0.164
1000GenomesGlobalStudy-wide5008T=0.855C=0.145
1000GenomesSouth AsianSub978T=0.870C=0.130
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.841C=0.159
The Genome Aggregation DatabaseAfricanSub8720T=0.875C=0.125
The Genome Aggregation DatabaseAmericanSub836T=0.600C=0.400
The Genome Aggregation DatabaseEast AsianSub1618T=0.980C=0.020
The Genome Aggregation DatabaseEuropeSub18480T=0.846C=0.153
The Genome Aggregation DatabaseGlobalStudy-wide29956T=0.855C=0.144
The Genome Aggregation DatabaseOtherSub302T=0.870C=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.855C=0.144
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.830C=0.170
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
rs108470230.0000838alcoholismpha002893
rs108470230.000084alcohol dependence20201924
rs108470230.00023alcohol dependence(early age of onset)20201924

eQTL of rs10847023 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 rs10847023 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 )
chr12126404519126404654E070-39866
chr12126404773126404935E070-39585
chr12126422187126422237E070-22283
chr12126422574126422652E070-21868
chr12126439015126439189E070-5331
chr12126439348126439845E070-4675
chr12126440725126441202E081-3318
chr12126470512126470775E08125992
chr12126404519126404654E082-39866
chr12126440725126441202E082-3318



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr12126467330126469317E06722810
chr12126467330126469317E06822810
chr12126467330126469317E07022810
chr12126469318126469380E07024798
chr12126469530126469693E07025010
chr12126467330126469317E07222810
chr12126469318126469380E07224798
chr12126469530126469693E07225010
chr12126467330126469317E07322810
chr12126469318126469380E07324798
chr12126469530126469693E07325010
chr12126467330126469317E08222810
chr12126469318126469380E08224798
chr12126469530126469693E08225010