rs11664080

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

TXNDC2 : Stop Gained

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0056 (1682/29984,GnomAD)
T=0055 (1628/29118,TOPMED)
C==0065 (851/13006,GO-ESP)
T=0063 (314/5008,1000G)
T=0069 (267/3854,ALSPAC)
T=0076 (281/3708,TWINSUK)

Position: chr18:9888030 (GRCh38.p7) (18p11.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 18	NC_000018.10:g.9888030C>A
GRCh38.p7 chr 18	NC_000018.10:g.9888030C>T
GRCh37.p13 chr 18	NC_000018.9:g.9888027C>A
GRCh37.p13 chr 18	NC_000018.9:g.9888027C>T

Gene: TXNDC2, thioredoxin domain containing 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TXNDC2 transcript variant 2	NM_001098529.1:c....NM_001098529.1:c.1551C>A	C [TGC]> * [TGA]	Coding Sequence Variant
thioredoxin domain-containing protein 2 isoform 2	NP_001091999.1:p....NP_001091999.1:p.Cys517Ter	C [Cys]> * [Ter]	Stop Gained
TXNDC2 transcript variant 2	NM_001098529.1:c....NM_001098529.1:c.1551C>T	C [TGC]> C [TGT]	Coding Sequence Variant
thioredoxin domain-containing protein 2 isoform 2	NP_001091999.1:p....NP_001091999.1:p.Cys517=	C [Cys]> C [Cys]	Synonymous Variant
TXNDC2 transcript variant 1	NM_032243.5:c.135...NM_032243.5:c.1350C>A	C [TGC]> * [TGA]	Coding Sequence Variant
thioredoxin domain-containing protein 2 isoform 1	NP_115619.4:p.Cys...NP_115619.4:p.Cys450Ter	C [Cys]> * [Ter]	Stop Gained
TXNDC2 transcript variant 1	NM_032243.5:c.135...NM_032243.5:c.1350C>T	C [TGC]> C [TGT]	Coding Sequence Variant
thioredoxin domain-containing protein 2 isoform 1	NP_115619.4:p.Cys...NP_115619.4:p.Cys450=	C [Cys]> C [Cys]	Synonymous Variant
TXNDC2 transcript variant X1	XM_017026041.1:c....XM_017026041.1:c.1350C>A	C [TGC]> * [TGA]	Coding Sequence Variant
thioredoxin domain-containing protein 2 isoform X1	XP_016881530.1:p....XP_016881530.1:p.Cys450Ter	C [Cys]> * [Ter]	Stop Gained
TXNDC2 transcript variant X1	XM_017026041.1:c....XM_017026041.1:c.1350C>T	C [TGC]> C [TGT]	Coding Sequence Variant
thioredoxin domain-containing protein 2 isoform X1	XP_016881530.1:p....XP_016881530.1:p.Cys450=	C [Cys]> C [Cys]	Synonymous Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.962	T=0.038
1000Genomes	American	Sub	694	C=0.940	T=0.060
1000Genomes	East Asian	Sub	1008	C=0.978	T=0.022
1000Genomes	Europe	Sub	1006	C=0.928	T=0.072
1000Genomes	Global	Study-wide	5008	C=0.937	T=0.063
1000Genomes	South Asian	Sub	978	C=0.870	T=0.130
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.931	T=0.069
The Genome Aggregation Database	African	Sub	8728	C=0.959	T=0.041
The Genome Aggregation Database	American	Sub	838	C=0.950	T=0.050
The Genome Aggregation Database	East Asian	Sub	1622	C=0.975	T=0.025
The Genome Aggregation Database	Europe	Sub	18494	C=0.934	T=0.065
The Genome Aggregation Database	Global	Study-wide	29984	C=0.943	T=0.056
The Genome Aggregation Database	Other	Sub	302	C=0.890	T=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.944	T=0.055
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.924	T=0.076

PMID	Title	Author	Journal
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs11664080	6.19E-05	alcohol dependence	19581569

eQTL of rs11664080 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 rs11664080 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.