rs1996017

Homo sapiens
T>C
TSHZ2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0326 (9748/29896,GnomAD)
T==0290 (8461/29118,TOPMED)
T==0383 (1918/5008,1000G)
T==0386 (1488/3854,ALSPAC)
T==0376 (1393/3708,TWINSUK)
chr20:53306099 (GRCh38.p7) (20q13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
38 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.53306099T>C
GRCh37.p13 chr 20NC_000020.10:g.51922638T>C

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
1000GenomesAfricanSub1322T=0.144C=0.856
1000GenomesAmericanSub694T=0.470C=0.530
1000GenomesEast AsianSub1008T=0.628C=0.372
1000GenomesEuropeSub1006T=0.394C=0.606
1000GenomesGlobalStudy-wide5008T=0.383C=0.617
1000GenomesSouth AsianSub978T=0.380C=0.620
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.386C=0.614
The Genome Aggregation DatabaseAfricanSub8706T=0.178C=0.822
The Genome Aggregation DatabaseAmericanSub836T=0.440C=0.560
The Genome Aggregation DatabaseEast AsianSub1606T=0.618C=0.382
The Genome Aggregation DatabaseEuropeSub18448T=0.366C=0.633
The Genome Aggregation DatabaseGlobalStudy-wide29896T=0.326C=0.673
The Genome Aggregation DatabaseOtherSub300T=0.260C=0.740
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.290C=0.709
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.376C=0.624
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
rs19960170.00046alcohol dependence20201924

eQTL of rs1996017 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 rs1996017 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 )
chr205193339851933459E07010760
chr205193354251933741E07010904
chr205193409051934241E07011452
chr205193424451934372E07011606
chr205194125151941313E07018613
chr205194136851941442E07018730
chr205194151351941613E07018875
chr205194190851942015E07019270
chr205194781851947960E07325180
chr205194797751948578E07325339
chr205189967751900066E081-22572
chr205190015451900246E081-22392
chr205190036751901297E081-21341
chr205190138751901634E081-21004
chr205190170851901812E081-20826
chr205191492751915003E081-7635
chr205191514851915198E081-7440
chr205191520051915240E081-7398
chr205191542551915481E081-7157
chr205191552251915776E081-6862
chr205191612151916385E081-6253
chr205191648751916716E081-5922
chr205191672451917033E081-5605
chr205191718951917244E081-5394
chr205191905051919152E081-3486
chr205191938451919518E081-3120
chr205196182251961909E08139184
chr205196205451962437E08139416
chr205196245351962922E08139815
chr205196294751963050E08140309
chr205196307251963266E08140434
chr205190015451900246E082-22392
chr205190036751901297E082-21341
chr205190138751901634E082-21004
chr205190170851901812E082-20826
chr205191672451917033E082-5605
chr205191905051919152E082-3486
chr205191938451919518E082-3120