rs3745720

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

TMEM143 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0378 (11327/29914,GnomAD)
C=0390 (11364/29118,TOPMED)
C=0354 (1771/5008,1000G)
C=0450 (1733/3854,ALSPAC)
C=0477 (1770/3708,TWINSUK)

Position: chr19:48332825 (GRCh38.p7) (19q13.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 32 Enhancers around

Promoter: 34 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.48332825A>C
GRCh37.p13 chr 19	NC_000019.9:g.48836082A>C

Molecule type	Change	Amino acid[Codon]	SO Term
TMEM143 transcript variant 4	NM_001303540.1:c.	N/A	3 Prime UTR Variant
TMEM143 transcript variant 3	NM_001303539.1:c.	N/A	3 Prime UTR Variant
TMEM143 transcript variant 1	NM_018273.3:c.	N/A	3 Prime UTR Variant
TMEM143 transcript variant 2	NM_001303538.1:c.	N/A	3 Prime UTR Variant
TMEM143 transcript variant 5	NR_130317.1:n.174...NR_130317.1:n.1745T>G	T>G	Non Coding Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.732	C=0.268
1000Genomes	American	Sub	694	A=0.590	C=0.410
1000Genomes	East Asian	Sub	1008	A=0.651	C=0.349
1000Genomes	Europe	Sub	1006	A=0.553	C=0.447
1000Genomes	Global	Study-wide	5008	A=0.646	C=0.354
1000Genomes	South Asian	Sub	978	A=0.660	C=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.550	C=0.450
The Genome Aggregation Database	African	Sub	8714	A=0.714	C=0.286
The Genome Aggregation Database	American	Sub	838	A=0.580	C=0.420
The Genome Aggregation Database	East Asian	Sub	1614	A=0.647	C=0.353
The Genome Aggregation Database	Europe	Sub	18446	A=0.579	C=0.420
The Genome Aggregation Database	Global	Study-wide	29914	A=0.621	C=0.378
The Genome Aggregation Database	Other	Sub	302	A=0.490	C=0.510
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.609	C=0.390
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.523	C=0.477

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs3745720	0.00085	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr19	48794926	48794984	E067	-41098
chr19	48794988	48795048	E067	-41034
chr19	48794926	48794984	E068	-41098
chr19	48794988	48795048	E068	-41034
chr19	48832332	48832452	E068	-3630
chr19	48844178	48844730	E068	8096
chr19	48854367	48855013	E068	18285
chr19	48843973	48844023	E069	7891
chr19	48844178	48844730	E069	8096
chr19	48851314	48851764	E069	15232
chr19	48834382	48834432	E070	-1650
chr19	48837884	48838184	E070	1802
chr19	48811343	48811393	E071	-24689
chr19	48811791	48812512	E071	-23570
chr19	48815984	48816069	E071	-20013
chr19	48816101	48816162	E071	-19920
chr19	48816235	48816348	E071	-19734
chr19	48823069	48824390	E071	-11692
chr19	48834382	48834432	E071	-1650
chr19	48851314	48851764	E071	15232
chr19	48811791	48812512	E072	-23570
chr19	48823069	48824390	E072	-11692
chr19	48823069	48824390	E073	-11692
chr19	48844178	48844730	E073	8096
chr19	48823069	48824390	E074	-11692
chr19	48834382	48834432	E074	-1650
chr19	48834382	48834432	E081	-1650
chr19	48835116	48835160	E081	-922
chr19	48853708	48853922	E081	17626
chr19	48854221	48854358	E081	18139
chr19	48844889	48844948	E082	8807
chr19	48845153	48845279	E082	9071

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	48824489	48826508	E067	-9574
chr19	48828209	48829721	E067	-6361
chr19	48832492	48834268	E067	-1814
chr19	48865848	48868596	E067	29766
chr19	48824489	48826508	E068	-9574
chr19	48828209	48829721	E068	-6361
chr19	48832492	48834268	E068	-1814
chr19	48865848	48868596	E068	29766
chr19	48824489	48826508	E069	-9574
chr19	48828209	48829721	E069	-6361
chr19	48832492	48834268	E069	-1814
chr19	48865848	48868596	E069	29766
chr19	48824489	48826508	E070	-9574
chr19	48828209	48829721	E070	-6361
chr19	48865848	48868596	E070	29766
chr19	48824489	48826508	E071	-9574
chr19	48828209	48829721	E071	-6361
chr19	48832492	48834268	E071	-1814
chr19	48865848	48868596	E071	29766
chr19	48824489	48826508	E072	-9574
chr19	48828209	48829721	E072	-6361
chr19	48832492	48834268	E072	-1814
chr19	48865848	48868596	E072	29766
chr19	48824489	48826508	E073	-9574
chr19	48828209	48829721	E073	-6361
chr19	48832492	48834268	E073	-1814
chr19	48865848	48868596	E073	29766
chr19	48824489	48826508	E074	-9574
chr19	48832492	48834268	E074	-1814
chr19	48865848	48868596	E074	29766
chr19	48824489	48826508	E082	-9574
chr19	48828209	48829721	E082	-6361
chr19	48832492	48834268	E082	-1814
chr19	48865848	48868596	E082	29766