rs4542003

Homo sapiens
T>C
LOC105376214 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0086 (2595/29926,GnomAD)
C=0101 (2959/29118,TOPMED)
C=0085 (424/5008,1000G)
C=0063 (244/3854,ALSPAC)
C=0065 (240/3708,TWINSUK)
chr9:108160738 (GRCh38.p7) (9q31.2)
AD
GWASdb2
1   publication(s)
See rs on genome
54 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.108160738T>C
GRCh37.p13 chr 9NC_000009.11:g.110923018T>C

Gene: LOC105376214, uncharacterized LOC105376214(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105376214 transcript variant X1XR_001746881.1:n.N/AIntron Variant
LOC105376214 transcript variant X2XR_001746882.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.846C=0.154
1000GenomesAmericanSub694T=0.950C=0.050
1000GenomesEast AsianSub1008T=0.985C=0.015
1000GenomesEuropeSub1006T=0.936C=0.064
1000GenomesGlobalStudy-wide5008T=0.915C=0.085
1000GenomesSouth AsianSub978T=0.890C=0.110
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.937C=0.063
The Genome Aggregation DatabaseAfricanSub8710T=0.856C=0.144
The Genome Aggregation DatabaseAmericanSub834T=0.950C=0.050
The Genome Aggregation DatabaseEast AsianSub1618T=0.995C=0.005
The Genome Aggregation DatabaseEuropeSub18462T=0.931C=0.068
The Genome Aggregation DatabaseGlobalStudy-wide29926T=0.913C=0.086
The Genome Aggregation DatabaseOtherSub302T=0.900C=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.898C=0.101
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.935C=0.065
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
rs45420030.00019alcohol dependence20201924

eQTL of rs4542003 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 rs4542003 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 )
chr9110904423110905551E067-17467
chr9110915781110915929E067-7089
chr9110949050110950053E06726032
chr9110969666110970473E06746648
chr9110904285110904390E068-18628
chr9110904423110905551E068-17467
chr9110905742110905796E068-17222
chr9110912998110913916E068-9102
chr9110969666110970473E06846648
chr9110904285110904390E069-18628
chr9110904423110905551E069-17467
chr9110948825110949001E06925807
chr9110949050110950053E06926032
chr9110950771110952024E06927753
chr9110904423110905551E070-17467
chr9110948699110948749E07025681
chr9110948825110949001E07025807
chr9110949050110950053E07026032
chr9110969666110970473E07046648
chr9110904423110905551E071-17467
chr9110912998110913916E071-9102
chr9110915781110915929E071-7089
chr9110916136110916412E071-6606
chr9110948825110949001E07125807
chr9110949050110950053E07126032
chr9110950771110952024E07127753
chr9110904423110905551E072-17467
chr9110905742110905796E072-17222
chr9110949050110950053E07226032
chr9110969666110970473E07246648
chr9110904423110905551E073-17467
chr9110969666110970473E07346648
chr9110903482110903536E074-19482
chr9110904103110904168E074-18850
chr9110904285110904390E074-18628
chr9110904423110905551E074-17467
chr9110905742110905796E074-17222
chr9110949050110950053E07426032
chr9110969666110970473E07446648
chr9110879500110880744E081-42274
chr9110880926110880982E081-42036
chr9110881484110881545E081-41473
chr9110904423110905551E081-17467
chr9110920534110920737E081-2281
chr9110920741110921156E081-1862
chr9110921351110921479E081-1539
chr9110879500110880744E082-42274
chr9110880926110880982E082-42036
chr9110899342110899805E082-23213
chr9110899878110899954E082-23064
chr9110900333110900387E082-22631
chr9110900400110900459E082-22559
chr9110904423110905551E082-17467
chr9110911821110911938E082-11080