rs830140

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SLC8A2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0215 (6447/29926,GnomAD)
A==0249 (7265/29118,TOPMED)
A==0263 (1319/5008,1000G)
A==0154 (592/3854,ALSPAC)
A==0153 (567/3708,TWINSUK)

Position: chr19:47444725 (GRCh38.p7) (19q13.32)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 158 Enhancers around

Promoter: 58 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.47444725A>G
GRCh37.p13 chr 19	NC_000019.9:g.47947982A>G

Gene: SLC8A2, solute carrier family 8 member A2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC8A2 transcript	NM_015063.2:c.	N/A	Intron Variant
SLC8A2 transcript variant X1	XM_005259172.1:c.	N/A	Intron Variant
SLC8A2 transcript variant X2	XM_017027159.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.393	G=0.607
1000Genomes	American	Sub	694	A=0.210	G=0.790
1000Genomes	East Asian	Sub	1008	A=0.227	G=0.773
1000Genomes	Europe	Sub	1006	A=0.144	G=0.856
1000Genomes	Global	Study-wide	5008	A=0.263	G=0.737
1000Genomes	South Asian	Sub	978	A=0.290	G=0.710
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.154	G=0.846
The Genome Aggregation Database	African	Sub	8714	A=0.361	G=0.639
The Genome Aggregation Database	American	Sub	838	A=0.190	G=0.810
The Genome Aggregation Database	East Asian	Sub	1610	A=0.224	G=0.776
The Genome Aggregation Database	Europe	Sub	18462	A=0.149	G=0.850
The Genome Aggregation Database	Global	Study-wide	29926	A=0.215	G=0.784
The Genome Aggregation Database	Other	Sub	302	A=0.070	G=0.930
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.249	G=0.750
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.153	G=0.847

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs830140	0.000563	alcohol dependence	24277619

eQTL of rs830140 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 rs830140 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 )
chr19	47939773	47940334	E067	-7648
chr19	47986419	47986555	E067	38437
chr19	47986598	47986685	E067	38616
chr19	47993264	47993410	E067	45282
chr19	47993438	47993551	E067	45456
chr19	47993575	47993674	E067	45593
chr19	47993790	47993903	E067	45808
chr19	47993950	47994085	E067	45968
chr19	47994108	47995019	E067	46126
chr19	47995076	47995259	E067	47094
chr19	47995276	47995806	E067	47294
chr19	47995872	47995954	E067	47890
chr19	47996012	47996063	E067	48030
chr19	47996094	47996474	E067	48112
chr19	47996545	47996957	E067	48563
chr19	47939773	47940334	E068	-7648
chr19	47946430	47946569	E068	-1413
chr19	47993264	47993410	E068	45282
chr19	47993438	47993551	E068	45456
chr19	47993575	47993674	E068	45593
chr19	47993790	47993903	E068	45808
chr19	47993950	47994085	E068	45968
chr19	47994108	47995019	E068	46126
chr19	47995076	47995259	E068	47094
chr19	47995276	47995806	E068	47294
chr19	47995872	47995954	E068	47890
chr19	47996012	47996063	E068	48030
chr19	47996094	47996474	E068	48112
chr19	47996545	47996957	E068	48563
chr19	47996961	47997051	E068	48979
chr19	47997075	47997410	E068	49093
chr19	47939773	47940334	E069	-7648
chr19	47993575	47993674	E069	45593
chr19	47993790	47993903	E069	45808
chr19	47993950	47994085	E069	45968
chr19	47994108	47995019	E069	46126
chr19	47995076	47995259	E069	47094
chr19	47995276	47995806	E069	47294
chr19	47995872	47995954	E069	47890
chr19	47996012	47996063	E069	48030
chr19	47996094	47996474	E069	48112
chr19	47902007	47902226	E070	-45756
chr19	47902316	47902891	E070	-45091
chr19	47926110	47926185	E070	-21797
chr19	47929767	47929877	E070	-18105
chr19	47929891	47930061	E070	-17921
chr19	47930104	47930269	E070	-17713
chr19	47930297	47930360	E070	-17622
chr19	47936418	47936628	E070	-11354
chr19	47940404	47940482	E070	-7500
chr19	47952275	47952475	E070	4293
chr19	47971155	47971560	E070	23173
chr19	47971741	47972624	E070	23759
chr19	47996961	47997051	E070	48979
chr19	47997075	47997410	E070	49093
chr19	47997656	47997710	E070	49674
chr19	47997878	47997928	E070	49896
chr19	47939520	47939769	E071	-8213
chr19	47939773	47940334	E071	-7648
chr19	47952275	47952475	E071	4293
chr19	47986598	47986685	E071	38616
chr19	47993575	47993674	E071	45593
chr19	47993790	47993903	E071	45808
chr19	47993950	47994085	E071	45968
chr19	47994108	47995019	E071	46126
chr19	47995076	47995259	E071	47094
chr19	47995276	47995806	E071	47294
chr19	47995872	47995954	E071	47890
chr19	47996012	47996063	E071	48030
chr19	47996094	47996474	E071	48112
chr19	47996545	47996957	E071	48563
chr19	47996961	47997051	E071	48979
chr19	47997075	47997410	E071	49093
chr19	47997656	47997710	E071	49674
chr19	47997878	47997928	E071	49896
chr19	47939773	47940334	E072	-7648
chr19	47940404	47940482	E072	-7500
chr19	47962777	47962909	E072	14795
chr19	47963153	47963210	E072	15171
chr19	47976031	47976124	E072	28049
chr19	47976215	47976332	E072	28233
chr19	47976382	47976432	E072	28400
chr19	47986419	47986555	E072	38437
chr19	47986598	47986685	E072	38616
chr19	47993264	47993410	E072	45282
chr19	47993438	47993551	E072	45456
chr19	47993575	47993674	E072	45593
chr19	47993790	47993903	E072	45808
chr19	47993950	47994085	E072	45968
chr19	47994108	47995019	E072	46126
chr19	47995076	47995259	E072	47094
chr19	47995276	47995806	E072	47294
chr19	47995872	47995954	E072	47890
chr19	47996545	47996957	E072	48563
chr19	47996961	47997051	E072	48979
chr19	47997075	47997410	E072	49093
chr19	47997656	47997710	E072	49674
chr19	47997878	47997928	E072	49896
chr19	47939773	47940334	E073	-7648
chr19	47952275	47952475	E073	4293
chr19	47952867	47952976	E073	4885
chr19	47952979	47953034	E073	4997
chr19	47962777	47962909	E073	14795
chr19	47986598	47986685	E073	38616
chr19	47992205	47992668	E073	44223
chr19	47992729	47992929	E073	44747
chr19	47992990	47993067	E073	45008
chr19	47993080	47993158	E073	45098
chr19	47993264	47993410	E073	45282
chr19	47993438	47993551	E073	45456
chr19	47993575	47993674	E073	45593
chr19	47993790	47993903	E073	45808
chr19	47993950	47994085	E073	45968
chr19	47994108	47995019	E073	46126
chr19	47995076	47995259	E073	47094
chr19	47995276	47995806	E073	47294
chr19	47995872	47995954	E073	47890
chr19	47996012	47996063	E073	48030
chr19	47996094	47996474	E073	48112
chr19	47996545	47996957	E073	48563
chr19	47996961	47997051	E073	48979
chr19	47997075	47997410	E073	49093
chr19	47997656	47997710	E073	49674
chr19	47997878	47997928	E073	49896
chr19	47993264	47993410	E074	45282
chr19	47993438	47993551	E074	45456
chr19	47993575	47993674	E074	45593
chr19	47993790	47993903	E074	45808
chr19	47993950	47994085	E074	45968
chr19	47919753	47919811	E081	-28171
chr19	47919820	47919901	E081	-28081
chr19	47939773	47940334	E081	-7648
chr19	47940404	47940482	E081	-7500
chr19	47962777	47962909	E081	14795
chr19	47967917	47968621	E081	19935
chr19	47969905	47969959	E081	21923
chr19	47971155	47971560	E081	23173
chr19	47971741	47972624	E081	23759
chr19	47972634	47973248	E081	24652
chr19	47973295	47973487	E081	25313
chr19	47973526	47973613	E081	25544
chr19	47986419	47986555	E081	38437
chr19	47986598	47986685	E081	38616
chr19	47997656	47997710	E081	49674
chr19	47997878	47997928	E081	49896
chr19	47919753	47919811	E082	-28171
chr19	47919820	47919901	E082	-28081
chr19	47926110	47926185	E082	-21797
chr19	47939773	47940334	E082	-7648
chr19	47962777	47962909	E082	14795
chr19	47963153	47963210	E082	15171
chr19	47969905	47969959	E082	21923
chr19	47971155	47971560	E082	23173
chr19	47996545	47996957	E082	48563
chr19	47996961	47997051	E082	48979
chr19	47997075	47997410	E082	49093
chr19	47997656	47997710	E082	49674
chr19	47997878	47997928	E082	49896

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	47920761	47922487	E067	-25495
chr19	47973687	47974058	E067	25705
chr19	47974077	47974149	E067	26095
chr19	47974249	47974420	E067	26267
chr19	47974465	47974653	E067	26483
chr19	47986705	47988035	E067	38723
chr19	47988043	47988121	E067	40061
chr19	47988141	47988282	E067	40159
chr19	47973687	47974058	E068	25705
chr19	47974077	47974149	E068	26095
chr19	47974249	47974420	E068	26267
chr19	47974465	47974653	E068	26483
chr19	47986705	47988035	E068	38723
chr19	47988043	47988121	E068	40061
chr19	47988141	47988282	E068	40159
chr19	47920761	47922487	E069	-25495
chr19	47973687	47974058	E069	25705
chr19	47974077	47974149	E069	26095
chr19	47974249	47974420	E069	26267
chr19	47974465	47974653	E069	26483
chr19	47986705	47988035	E069	38723
chr19	47988043	47988121	E069	40061
chr19	47988141	47988282	E069	40159
chr19	47920761	47922487	E070	-25495
chr19	47922513	47923056	E070	-24926
chr19	47986705	47988035	E070	38723
chr19	47920761	47922487	E071	-25495
chr19	47973687	47974058	E071	25705
chr19	47974077	47974149	E071	26095
chr19	47974249	47974420	E071	26267
chr19	47974465	47974653	E071	26483
chr19	47986705	47988035	E071	38723
chr19	47988043	47988121	E071	40061
chr19	47988141	47988282	E071	40159
chr19	47920761	47922487	E072	-25495
chr19	47973687	47974058	E072	25705
chr19	47974077	47974149	E072	26095
chr19	47974249	47974420	E072	26267
chr19	47974465	47974653	E072	26483
chr19	47986705	47988035	E072	38723
chr19	47988043	47988121	E072	40061
chr19	47988141	47988282	E072	40159
chr19	47973687	47974058	E073	25705
chr19	47974077	47974149	E073	26095
chr19	47974249	47974420	E073	26267
chr19	47974465	47974653	E073	26483
chr19	47986705	47988035	E073	38723
chr19	47988043	47988121	E073	40061
chr19	47986705	47988035	E074	38723
chr19	47988043	47988121	E074	40061
chr19	47988141	47988282	E074	40159
chr19	47920761	47922487	E081	-25495
chr19	47986705	47988035	E081	38723
chr19	47920761	47922487	E082	-25495
chr19	47922513	47923056	E082	-24926
chr19	47986705	47988035	E082	38723
chr19	47988043	47988121	E082	40061
chr19	47988141	47988282	E082	40159