rs6022378

Homo sapiens
A>G
TSHZ2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0367 (10993/29912,GnomAD)
A==0345 (10045/29118,TOPMED)
A==0428 (2142/5008,1000G)
A==0391 (1508/3854,ALSPAC)
A==0383 (1420/3708,TWINSUK)
chr20:53300709 (GRCh38.p7) (20q13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
38 Enhancers around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.53300709A>G
GRCh37.p13 chr 20NC_000020.10:g.51917248A>G

Gene: TSHZ2, teashirt zinc finger homeobox 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TSHZ2 transcript variant 2NM_001193421.1:c.N/AIntron Variant
TSHZ2 transcript variant 1NM_173485.5:c.N/AIntron Variant
TSHZ2 transcript variant X1XM_017027640.1:c.N/AIntron Variant
TSHZ2 transcript variant X2XM_017027641.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.305G=0.695
1000GenomesAmericanSub694A=0.480G=0.520
1000GenomesEast AsianSub1008A=0.638G=0.362
1000GenomesEuropeSub1006A=0.401G=0.599
1000GenomesGlobalStudy-wide5008A=0.428G=0.572
1000GenomesSouth AsianSub978A=0.370G=0.630
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.391G=0.609
The Genome Aggregation DatabaseAfricanSub8694A=0.300G=0.700
The Genome Aggregation DatabaseAmericanSub838A=0.450G=0.550
The Genome Aggregation DatabaseEast AsianSub1620A=0.627G=0.373
The Genome Aggregation DatabaseEuropeSub18458A=0.374G=0.625
The Genome Aggregation DatabaseGlobalStudy-wide29912A=0.367G=0.632
The Genome Aggregation DatabaseOtherSub302A=0.260G=0.740
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.345G=0.655
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.383G=0.617
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
rs60223780.00052alcohol dependence20201924

eQTL of rs6022378 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 rs6022378 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 )
chr205193339851933459E07016150
chr205193354251933741E07016294
chr205193409051934241E07016842
chr205193424451934372E07016996
chr205194125151941313E07024003
chr205194136851941442E07024120
chr205194151351941613E07024265
chr205194190851942015E07024660
chr205194781851947960E07330570
chr205194797751948578E07330729
chr205189967751900066E081-17182
chr205190015451900246E081-17002
chr205190036751901297E081-15951
chr205190138751901634E081-15614
chr205190170851901812E081-15436
chr205191492751915003E081-2245
chr205191514851915198E081-2050
chr205191520051915240E081-2008
chr205191542551915481E081-1767
chr205191552251915776E081-1472
chr205191612151916385E081-863
chr205191648751916716E081-532
chr205191672451917033E081-215
chr205191718951917244E081-4
chr205191905051919152E0811802
chr205191938451919518E0812136
chr205196182251961909E08144574
chr205196205451962437E08144806
chr205196245351962922E08145205
chr205196294751963050E08145699
chr205196307251963266E08145824
chr205190015451900246E082-17002
chr205190036751901297E082-15951
chr205190138751901634E082-15614
chr205190170851901812E082-15436
chr205191672451917033E082-215
chr205191905051919152E0821802
chr205191938451919518E0822136




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr205187116851871208E074-46040
chr205187127651871336E074-45912