rs1543080

Homo sapiens
C>A
TSHZ2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0134 (4027/29964,GnomAD)
A=0163 (4754/29118,TOPMED)
A=0177 (884/5008,1000G)
A=0085 (326/3854,ALSPAC)
A=0088 (326/3708,TWINSUK)
chr20:53280576 (GRCh38.p7) (20q13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
31 Enhancers around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.53280576C>A
GRCh37.p13 chr 20NC_000020.10:g.51897115C>A

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
1000GenomesAfricanSub1322C=0.755A=0.245
1000GenomesAmericanSub694C=0.790A=0.210
1000GenomesEast AsianSub1008C=0.843A=0.157
1000GenomesEuropeSub1006C=0.905A=0.095
1000GenomesGlobalStudy-wide5008C=0.823A=0.177
1000GenomesSouth AsianSub978C=0.830A=0.170
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.915A=0.085
The Genome Aggregation DatabaseAfricanSub8714C=0.782A=0.218
The Genome Aggregation DatabaseAmericanSub838C=0.750A=0.250
The Genome Aggregation DatabaseEast AsianSub1618C=0.849A=0.151
The Genome Aggregation DatabaseEuropeSub18492C=0.910A=0.089
The Genome Aggregation DatabaseGlobalStudy-wide29964C=0.865A=0.134
The Genome Aggregation DatabaseOtherSub302C=0.920A=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.836A=0.163
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.912A=0.088
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
rs15430805.59E-05alcohol dependence21314694

eQTL of rs1543080 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 rs1543080 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 )
chr205193339851933459E07036283
chr205193354251933741E07036427
chr205193409051934241E07036975
chr205193424451934372E07037129
chr205194125151941313E07044136
chr205194136851941442E07044253
chr205194151351941613E07044398
chr205194190851942015E07044793
chr205189967751900066E0812562
chr205190015451900246E0813039
chr205190036751901297E0813252
chr205190138751901634E0814272
chr205190170851901812E0814593
chr205191492751915003E08117812
chr205191514851915198E08118033
chr205191520051915240E08118085
chr205191542551915481E08118310
chr205191552251915776E08118407
chr205191612151916385E08119006
chr205191648751916716E08119372
chr205191672451917033E08119609
chr205191718951917244E08120074
chr205191905051919152E08121935
chr205191938451919518E08122269
chr205190015451900246E0823039
chr205190036751901297E0823252
chr205190138751901634E0824272
chr205190170851901812E0824593
chr205191672451917033E08219609
chr205191905051919152E08221935
chr205191938451919518E08222269



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr205187116851871208E074-25907
chr205187127651871336E074-25779