rs2489188

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

TGFBR3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0354 (10616/29930,GnomAD)
C==0359 (10479/29118,TOPMED)
C==0316 (1585/5008,1000G)
C==0324 (1250/3854,ALSPAC)
C==0329 (1219/3708,TWINSUK)

Position: chr1:91866932 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 65 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.91866932C>T
GRCh37.p13 chr 1	NC_000001.10:g.92332489C>T
TGFBR3 RefSeqGene	NG_027757.1:g.44071G>A

Gene: TGFBR3, transforming growth factor beta receptor 3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TGFBR3 transcript variant 2	NM_001195683.1:c.	N/A	Intron Variant
TGFBR3 transcript variant 3	NM_001195684.1:c.	N/A	Intron Variant
TGFBR3 transcript variant 1	NM_003243.4:c.	N/A	Intron Variant
TGFBR3 transcript variant 4	NR_036634.1:n.	N/A	Intron Variant
TGFBR3 transcript variant X1	XM_006710867.2:c.	N/A	Intron Variant
TGFBR3 transcript variant X2	XM_006710868.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.390	T=0.610
1000Genomes	American	Sub	694	C=0.300	T=0.700
1000Genomes	East Asian	Sub	1008	C=0.214	T=0.786
1000Genomes	Europe	Sub	1006	C=0.349	T=0.651
1000Genomes	Global	Study-wide	5008	C=0.316	T=0.684
1000Genomes	South Asian	Sub	978	C=0.300	T=0.700
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.324	T=0.676
The Genome Aggregation Database	African	Sub	8714	C=0.381	T=0.619
The Genome Aggregation Database	American	Sub	834	C=0.320	T=0.680
The Genome Aggregation Database	East Asian	Sub	1612	C=0.213	T=0.787
The Genome Aggregation Database	Europe	Sub	18468	C=0.355	T=0.644
The Genome Aggregation Database	Global	Study-wide	29930	C=0.354	T=0.645
The Genome Aggregation Database	Other	Sub	302	C=0.390	T=0.610
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.359	T=0.640
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.329	T=0.671

PMID	Title	Author	Journal
22440163	Association analysis of TGFBR3 gene with Vogt-Koyanagi-Harada disease and Behcet's disease in the Chinese Han population.	Chen Y	Curr Eye Res
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs2489188	0.000909	alcohol dependence	21314694

eQTL of rs2489188 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 rs2489188 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 )
chr1	92282538	92283429	E067	-49060
chr1	92292651	92293735	E067	-38754
chr1	92295723	92296422	E067	-36067
chr1	92296441	92296971	E067	-35518
chr1	92348365	92348415	E067	15876
chr1	92282538	92283429	E068	-49060
chr1	92283887	92284066	E068	-48423
chr1	92284108	92284336	E068	-48153
chr1	92292651	92293735	E068	-38754
chr1	92293741	92294122	E068	-38367
chr1	92295723	92296422	E068	-36067
chr1	92296441	92296971	E068	-35518
chr1	92310447	92311084	E068	-21405
chr1	92316672	92317495	E068	-14994
chr1	92284108	92284336	E069	-48153
chr1	92292651	92293735	E069	-38754
chr1	92295723	92296422	E069	-36067
chr1	92296441	92296971	E069	-35518
chr1	92312184	92312314	E069	-20175
chr1	92316672	92317495	E069	-14994
chr1	92346602	92346707	E069	14113
chr1	92346875	92347082	E069	14386
chr1	92295723	92296422	E070	-36067
chr1	92310447	92311084	E070	-21405
chr1	92311137	92311278	E070	-21211
chr1	92311303	92312128	E070	-20361
chr1	92292651	92293735	E071	-38754
chr1	92295484	92295690	E071	-36799
chr1	92295723	92296422	E071	-36067
chr1	92296441	92296971	E071	-35518
chr1	92296994	92297163	E071	-35326
chr1	92297252	92297302	E071	-35187
chr1	92297342	92297393	E071	-35096
chr1	92311137	92311278	E071	-21211
chr1	92311303	92312128	E071	-20361
chr1	92312184	92312314	E071	-20175
chr1	92283463	92283872	E072	-48617
chr1	92283887	92284066	E072	-48423
chr1	92284108	92284336	E072	-48153
chr1	92295723	92296422	E072	-36067
chr1	92296441	92296971	E072	-35518
chr1	92296994	92297163	E072	-35326
chr1	92316399	92316619	E072	-15870
chr1	92316672	92317495	E072	-14994
chr1	92317518	92317558	E072	-14931
chr1	92317871	92317940	E072	-14549
chr1	92282538	92283429	E073	-49060
chr1	92283463	92283872	E073	-48617
chr1	92283887	92284066	E073	-48423
chr1	92284108	92284336	E073	-48153
chr1	92292651	92293735	E073	-38754
chr1	92293741	92294122	E073	-38367
chr1	92294231	92294465	E073	-38024
chr1	92294484	92294698	E073	-37791
chr1	92295723	92296422	E073	-36067
chr1	92296441	92296971	E073	-35518
chr1	92311137	92311278	E073	-21211
chr1	92311303	92312128	E073	-20361
chr1	92312184	92312314	E073	-20175
chr1	92312316	92312451	E073	-20038
chr1	92312459	92312640	E073	-19849
chr1	92292651	92293735	E074	-38754
chr1	92296441	92296971	E074	-35518
chr1	92316399	92316619	E074	-15870
chr1	92316672	92317495	E074	-14994

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	92349899	92352783	E067	17410
chr1	92349899	92352783	E068	17410
chr1	92349899	92352783	E069	17410
chr1	92349723	92349796	E071	17234
chr1	92349899	92352783	E071	17410
chr1	92349899	92352783	E072	17410
chr1	92349899	92352783	E073	17410
chr1	92349899	92352783	E074	17410
chr1	92349899	92352783	E082	17410