rs4413346

Homo sapiens
T>C
None
Check p-value
SNV (Single Nucleotide Variation)
C=0250 (7490/29910,GnomAD)
C=0265 (7719/29118,TOPMED)
C=0182 (912/5008,1000G)
C=0286 (1103/3854,ALSPAC)
C=0284 (1054/3708,TWINSUK)
chr3:121767463 (GRCh38.p7) (3q13.33)
AD
GWASdb2
1   publication(s)
See rs on genome
19 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.121767463T>C
GRCh37.p13 chr 3NC_000003.11:g.121486310T>C

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.734C=0.266
1000GenomesAmericanSub694T=0.860C=0.140
1000GenomesEast AsianSub1008T=0.907C=0.093
1000GenomesEuropeSub1006T=0.725C=0.275
1000GenomesGlobalStudy-wide5008T=0.818C=0.182
1000GenomesSouth AsianSub978T=0.910C=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.714C=0.286
The Genome Aggregation DatabaseAfricanSub8694T=0.743C=0.257
The Genome Aggregation DatabaseAmericanSub838T=0.860C=0.140
The Genome Aggregation DatabaseEast AsianSub1622T=0.925C=0.075
The Genome Aggregation DatabaseEuropeSub18454T=0.731C=0.268
The Genome Aggregation DatabaseGlobalStudy-wide29910T=0.749C=0.250
The Genome Aggregation DatabaseOtherSub302T=0.790C=0.210
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.734C=0.265
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.716C=0.284
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
rs44133460.000968alcohol dependence21314694

eQTL of rs4413346 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr3:121486310IQCB1ENSG00000173226.12T>C4.8526e-12-67616Cerebellum
Chr3:121486310SLC15A2ENSG00000163406.6T>C7.5866e-24-126626Cerebellum
Chr3:121486310IQCB1ENSG00000173226.12T>C1.3081e-7-67616Frontal_Cortex_BA9
Chr3:121486310IQCB1ENSG00000173226.12T>C3.5378e-6-67616Hypothalamus
Chr3:121486310IQCB1ENSG00000173226.12T>C2.2547e-11-67616Cortex
Chr3:121486310IQCB1ENSG00000173226.12T>C2.9963e-10-67616Cerebellar_Hemisphere
Chr3:121486310SLC15A2ENSG00000163406.6T>C6.8466e-9-126626Cerebellar_Hemisphere
Chr3:121486310IQCB1ENSG00000173226.12T>C1.7752e-11-67616Caudate_basal_ganglia
Chr3:121486310IQCB1ENSG00000173226.12T>C1.8333e-6-67616Hippocampus
Chr3:121486310IQCB1ENSG00000173226.12T>C7.9988e-5-67616Substantia_nigra
Chr3:121486310IQCB1ENSG00000173226.12T>C2.2446e-9-67616Putamen_basal_ganglia
Chr3:121486310IQCB1ENSG00000173226.12T>C9.6301e-11-67616Anterior_cingulate_cortex
Chr3:121486310IQCB1ENSG00000173226.12T>C3.1161e-9-67616Nucleus_accumbens_basal_ganglia

meQTL of rs4413346 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 )
chr3121450303121450434E067-35876
chr3121465061121465101E067-21209
chr3121449490121449548E068-36762
chr3121450303121450434E068-35876
chr3121464433121464483E068-21827
chr3121449490121449548E071-36762
chr3121453657121453807E071-32503
chr3121454102121454207E071-32103
chr3121465061121465101E071-21209
chr3121465580121465692E071-20618
chr3121449490121449548E072-36762
chr3121450303121450434E072-35876
chr3121464433121464483E072-21827
chr3121465061121465101E072-21209
chr3121465580121465692E072-20618
chr3121450303121450434E073-35876
chr3121449490121449548E074-36762
chr3121450303121450434E074-35876
chr3121465061121465101E082-21209







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3121467470121469352E067-16958
chr3121467470121469352E068-16958
chr3121467470121469352E069-16958
chr3121467470121469352E070-16958
chr3121467470121469352E071-16958
chr3121467470121469352E072-16958
chr3121467470121469352E073-16958
chr3121467470121469352E074-16958
chr3121467470121469352E081-16958
chr3121467470121469352E082-16958