rs4809760

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SLC9A8 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0449 (13440/29902,GnomAD)
A==0495 (14416/29118,TOPMED)
G=0451 (2261/5008,1000G)
G=0408 (1574/3854,ALSPAC)
G=0401 (1488/3708,TWINSUK)

Position: chr20:49838134 (GRCh38.p7) (20q13.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 91 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.49838134A>G
GRCh37.p13 chr 20	NC_000020.10:g.48454671A>G

Gene: SLC9A8, solute carrier family 9 member A8(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC9A8 transcript variant 1	NM_001260491.1:c.	N/A	Intron Variant
SLC9A8 transcript variant 2	NM_015266.2:c.	N/A	Intron Variant
SLC9A8 transcript variant 3	NR_048537.1:n.	N/A	Intron Variant
SLC9A8 transcript variant 4	NR_048538.1:n.	N/A	Intron Variant
SLC9A8 transcript variant 5	NR_048539.1:n.	N/A	Intron Variant
SLC9A8 transcript variant 6	NR_048540.1:n.	N/A	Intron Variant
SLC9A8 transcript variant X2	XM_006723756.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X1	XM_011528736.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X3	XM_011528737.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X4	XM_011528738.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X5	XM_011528739.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X7	XM_011528740.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X8	XM_011528741.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X10	XM_011528742.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X14	XM_011528745.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X6	XM_017027754.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X9	XM_017027755.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X12	XM_017027756.1:c.	N/A	Intron Variant
SLC9A8 transcript variant X11	XM_011528743.2:c.	N/A	Genic Upstream Transcript Variant
SLC9A8 transcript variant X13	XM_011528744.2:c.	N/A	Genic Upstream Transcript 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=0.610	G=0.390
1000Genomes	East Asian	Sub	1008	A=0.490	G=0.510
1000Genomes	Europe	Sub	1006	A=0.571	G=0.429
1000Genomes	Global	Study-wide	5008	A=0.549	G=0.451
1000Genomes	South Asian	Sub	978	A=0.750	G=0.250
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.592	G=0.408
The Genome Aggregation Database	African	Sub	8696	A=0.409	G=0.591
The Genome Aggregation Database	American	Sub	832	A=0.640	G=0.360
The Genome Aggregation Database	East Asian	Sub	1614	A=0.488	G=0.512
The Genome Aggregation Database	Europe	Sub	18458	A=0.617	G=0.382
The Genome Aggregation Database	Global	Study-wide	29902	A=0.550	G=0.449
The Genome Aggregation Database	Other	Sub	302	A=0.600	G=0.400
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.495	G=0.504
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.599	G=0.401

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

P-Value

SNP ID	p-value	Traits	Study
rs4809760	0.00025	alcohol dependence	20201924

eQTL of rs4809760 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr20:48454671	SLC9A8	ENSG00000197818.7	A>G	2.4780e-11	25421	Cerebellum
Chr20:48454671	SLC9A8	ENSG00000197818.7	A>G	1.9733e-8	25421	Cerebellar_Hemisphere

meQTL of rs4809760 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 )
chr20	48466821	48467353	E067	12150
chr20	48467380	48467443	E067	12709
chr20	48467450	48467740	E067	12779
chr20	48467755	48468209	E067	13084
chr20	48468233	48468545	E067	13562
chr20	48468606	48468760	E067	13935
chr20	48468887	48468988	E067	14216
chr20	48469193	48469318	E067	14522
chr20	48484840	48484954	E067	30169
chr20	48485088	48485254	E067	30417
chr20	48503304	48503454	E067	48633
chr20	48466821	48467353	E068	12150
chr20	48467380	48467443	E068	12709
chr20	48467450	48467740	E068	12779
chr20	48467755	48468209	E068	13084
chr20	48468233	48468545	E068	13562
chr20	48468606	48468760	E068	13935
chr20	48468887	48468988	E068	14216
chr20	48469193	48469318	E068	14522
chr20	48470211	48470679	E068	15540
chr20	48470759	48471100	E068	16088
chr20	48471104	48471390	E068	16433
chr20	48484840	48484954	E068	30169
chr20	48485088	48485254	E068	30417
chr20	48485645	48485705	E068	30974
chr20	48494437	48494644	E068	39766
chr20	48467380	48467443	E069	12709
chr20	48467450	48467740	E069	12779
chr20	48467755	48468209	E069	13084
chr20	48468233	48468545	E069	13562
chr20	48468606	48468760	E069	13935
chr20	48468887	48468988	E069	14216
chr20	48469193	48469318	E069	14522
chr20	48493958	48494358	E069	39287
chr20	48503304	48503454	E069	48633
chr20	48446945	48446995	E071	-7676
chr20	48448830	48449150	E071	-5521
chr20	48467755	48468209	E071	13084
chr20	48468233	48468545	E071	13562
chr20	48468606	48468760	E071	13935
chr20	48468887	48468988	E071	14216
chr20	48469193	48469318	E071	14522
chr20	48502787	48502955	E071	48116
chr20	48502990	48503040	E071	48319
chr20	48503099	48503239	E071	48428
chr20	48503304	48503454	E071	48633
chr20	48448830	48449150	E072	-5521
chr20	48466821	48467353	E072	12150
chr20	48467380	48467443	E072	12709
chr20	48467450	48467740	E072	12779
chr20	48467755	48468209	E072	13084
chr20	48468233	48468545	E072	13562
chr20	48468606	48468760	E072	13935
chr20	48468887	48468988	E072	14216
chr20	48469193	48469318	E072	14522
chr20	48502990	48503040	E072	48319
chr20	48503099	48503239	E072	48428
chr20	48503304	48503454	E072	48633
chr20	48448367	48448773	E073	-5898
chr20	48467450	48467740	E073	12779
chr20	48467755	48468209	E073	13084
chr20	48468233	48468545	E073	13562
chr20	48468606	48468760	E073	13935
chr20	48484144	48484247	E073	29473
chr20	48484470	48484642	E073	29799
chr20	48484840	48484954	E073	30169
chr20	48485088	48485254	E073	30417
chr20	48502787	48502955	E073	48116
chr20	48502990	48503040	E073	48319
chr20	48503099	48503239	E073	48428
chr20	48503304	48503454	E073	48633
chr20	48446570	48446620	E074	-8051
chr20	48446796	48446878	E074	-7793
chr20	48446945	48446995	E074	-7676
chr20	48466821	48467353	E074	12150
chr20	48467380	48467443	E074	12709
chr20	48467450	48467740	E074	12779
chr20	48467755	48468209	E074	13084
chr20	48468233	48468545	E074	13562
chr20	48468606	48468760	E074	13935
chr20	48468887	48468988	E074	14216
chr20	48469193	48469318	E074	14522
chr20	48484840	48484954	E074	30169
chr20	48485088	48485254	E074	30417
chr20	48502656	48502746	E081	47985
chr20	48502787	48502955	E081	48116
chr20	48502990	48503040	E081	48319
chr20	48503099	48503239	E081	48428
chr20	48503304	48503454	E081	48633
chr20	48503099	48503239	E082	48428
chr20	48503304	48503454	E082	48633

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr20	48428217	48430084	E067	-24587
chr20	48428217	48430084	E068	-24587
chr20	48428217	48430084	E069	-24587
chr20	48428217	48430084	E070	-24587
chr20	48428217	48430084	E071	-24587
chr20	48428217	48430084	E072	-24587
chr20	48428217	48430084	E073	-24587
chr20	48428217	48430084	E074	-24587
chr20	48428217	48430084	E081	-24587
chr20	48428217	48430084	E082	-24587