rs13029542

Homo sapiens
C>T
MIR217HG : Intron Variant
MIR216B : 2KB Upstream Variant
LOC105374690 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0360 (10777/29908,GnomAD)
T=0454 (13238/29116,TOPMED)
T=0378 (1892/5008,1000G)
T=0280 (1078/3854,ALSPAC)
T=0291 (1079/3708,TWINSUK)
chr2:56001216 (GRCh38.p7) (2p16.1)
AD
GWASdb2
1   publication(s)
See rs on genome
31 Enhancers around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.56001216C>T
GRCh37.p13 chr 2NC_000002.11:g.56228351C>T

Gene: MIR217HG, MIR217 host gene(minus strand)

Molecule type Change Amino acid[Codon] SO Term
MIR217HG transcriptNR_126406.1:n.N/AIntron Variant

Gene: MIR216B, microRNA 216b(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
MIR216B transcriptNR_030623.1:n.N/AUpstream Transcript Variant

Gene: LOC105374690, uncharacterized LOC105374690(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105374690 transcriptXR_940109.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.254T=0.746
1000GenomesAmericanSub694C=0.740T=0.260
1000GenomesEast AsianSub1008C=0.944T=0.056
1000GenomesEuropeSub1006C=0.726T=0.274
1000GenomesGlobalStudy-wide5008C=0.622T=0.378
1000GenomesSouth AsianSub978C=0.600T=0.400
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.720T=0.280
The Genome Aggregation DatabaseAfricanSub8716C=0.323T=0.677
The Genome Aggregation DatabaseAmericanSub834C=0.790T=0.210
The Genome Aggregation DatabaseEast AsianSub1614C=0.959T=0.041
The Genome Aggregation DatabaseEuropeSub18442C=0.753T=0.246
The Genome Aggregation DatabaseGlobalStudy-wide29908C=0.639T=0.360
The Genome Aggregation DatabaseOtherSub302C=0.700T=0.300
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.545T=0.454
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.709T=0.291
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
rs130295420.00043alcohol dependence20201924

eQTL of rs13029542 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 rs13029542 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 )
chr25623545556235706E0677104
chr25623589556236097E0677544
chr25623624756236597E0677896
chr25619308356194079E068-34272
chr25623545556235706E0687104
chr25623545556235706E0697104
chr25623589556236097E0697544
chr25623545556235706E0707104
chr25623589556236097E0707544
chr25619308356194079E071-34272
chr25623545556235706E0717104
chr25624289156242941E07114540
chr25624297556243076E07114624
chr25619308356194079E072-34272
chr25623545556235706E0727104
chr25623589556236097E0727544
chr25624496456245014E07216613
chr25624505556245107E07216704
chr25624511056245199E07216759
chr25624530456245682E07216953
chr25623545556235706E0747104
chr25623589556236097E0747544
chr25623624756236597E0747896
chr25624496456245014E07416613
chr25624505556245107E07416704
chr25624511056245199E07416759
chr25624530456245682E07416953
chr25623589556236097E0817544
chr25623624756236597E0817896
chr25624109156241281E08212740
chr25624139156241475E08213040









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr25624581756245965E07117466
chr25624581756245965E07417466