rs4553860

Homo sapiens
A>G
MIR217HG : Intron Variant
LOC105374690 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0282 (8449/29896,GnomAD)
G=0349 (10172/29116,TOPMED)
G=0296 (1484/5008,1000G)
G=0236 (909/3854,ALSPAC)
G=0246 (912/3708,TWINSUK)
chr2:56016961 (GRCh38.p7) (2p16.1)
AD
GWASdb2
1   publication(s)
See rs on genome
28 Enhancers around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.56016961A>G
GRCh37.p13 chr 2NC_000002.11:g.56244096A>G

Gene: MIR217HG, MIR217 host gene(minus strand)

Molecule type Change Amino acid[Codon] SO Term
MIR217HG transcriptNR_126406.1:n.N/AIntron 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
1000GenomesAfricanSub1322A=0.465G=0.535
1000GenomesAmericanSub694A=0.790G=0.210
1000GenomesEast AsianSub1008A=0.944G=0.056
1000GenomesEuropeSub1006A=0.772G=0.228
1000GenomesGlobalStudy-wide5008A=0.704G=0.296
1000GenomesSouth AsianSub978A=0.640G=0.360
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.764G=0.236
The Genome Aggregation DatabaseAfricanSub8704A=0.506G=0.494
The Genome Aggregation DatabaseAmericanSub836A=0.830G=0.170
The Genome Aggregation DatabaseEast AsianSub1616A=0.959G=0.041
The Genome Aggregation DatabaseEuropeSub18438A=0.790G=0.209
The Genome Aggregation DatabaseGlobalStudy-wide29896A=0.717G=0.282
The Genome Aggregation DatabaseOtherSub302A=0.750G=0.250
Trans-Omics for Precision MedicineGlobalStudy-wide29116A=0.650G=0.349
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.754G=0.246
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
rs45538600.00049alcohol dependence20201924

eQTL of rs4553860 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 rs4553860 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 )
chr25623545556235706E067-8390
chr25623589556236097E067-7999
chr25623624756236597E067-7499
chr25623545556235706E068-8390
chr25623545556235706E069-8390
chr25623589556236097E069-7999
chr25623545556235706E070-8390
chr25623589556236097E070-7999
chr25623545556235706E071-8390
chr25624289156242941E071-1155
chr25624297556243076E071-1020
chr25623545556235706E072-8390
chr25623589556236097E072-7999
chr25624496456245014E072868
chr25624505556245107E072959
chr25624511056245199E0721014
chr25624530456245682E0721208
chr25623545556235706E074-8390
chr25623589556236097E074-7999
chr25623624756236597E074-7499
chr25624496456245014E074868
chr25624505556245107E074959
chr25624511056245199E0741014
chr25624530456245682E0741208
chr25623589556236097E081-7999
chr25623624756236597E081-7499
chr25624109156241281E082-2815
chr25624139156241475E082-2621









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr25624581756245965E0711721
chr25624581756245965E0741721