rs10939500

Homo sapiens
C>A
LINC01182 : Intron Variant
LOC107986184 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0202 (6053/29942,GnomAD)
A=0186 (5436/29118,TOPMED)
A=0170 (849/5008,1000G)
A=0253 (976/3854,ALSPAC)
A=0280 (1040/3708,TWINSUK)
chr4:13713497 (GRCh38.p7) (4p15.33)
AD
GWASdb2
1   publication(s)
See rs on genome
1 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.13713497C>A
GRCh37.p13 chr 4NC_000004.11:g.13715121C>A

Gene: LINC01182, long intergenic non-protein coding RNA 1182(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01182 transcriptNR_121681.1:n.N/AIntron Variant

Gene: LOC107986184, uncharacterized LOC107986184(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107986184 transcriptXR_001741389.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.871A=0.129
1000GenomesAmericanSub694C=0.790A=0.210
1000GenomesEast AsianSub1008C=0.990A=0.010
1000GenomesEuropeSub1006C=0.751A=0.249
1000GenomesGlobalStudy-wide5008C=0.830A=0.170
1000GenomesSouth AsianSub978C=0.720A=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.747A=0.253
The Genome Aggregation DatabaseAfricanSub8710C=0.861A=0.139
The Genome Aggregation DatabaseAmericanSub834C=0.770A=0.230
The Genome Aggregation DatabaseEast AsianSub1620C=0.991A=0.009
The Genome Aggregation DatabaseEuropeSub18476C=0.751A=0.248
The Genome Aggregation DatabaseGlobalStudy-wide29942C=0.797A=0.202
The Genome Aggregation DatabaseOtherSub302C=0.850A=0.150
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.813A=0.186
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.720A=0.280
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs109395000.000391alcohol dependence21314694

eQTL of rs10939500 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 rs10939500 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 )
chr41370710213708204E068-6917