rs1446890

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

EXOC6B : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0142 (4272/29946,GnomAD)
G==0174 (5068/29116,TOPMED)
G==0118 (591/5008,1000G)
G==0114 (438/3854,ALSPAC)
G==0119 (443/3708,TWINSUK)

Position: chr2:72568601 (GRCh38.p7) (2p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 68 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.72568601G>A
GRCh37.p13 chr 2	NC_000002.11:g.72795730G>A

Gene: EXOC6B, exocyst complex component 6B(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EXOC6B transcript variant 1	NM_001321729.1:c.	N/A	Intron Variant
EXOC6B transcript variant 3	NM_001321730.1:c.	N/A	Intron Variant
EXOC6B transcript variant 4	NM_001321731.1:c.	N/A	Intron Variant
EXOC6B transcript variant 5	NM_001321733.1:c.	N/A	Intron Variant
EXOC6B transcript variant 6	NM_001321734.1:c.	N/A	Intron Variant
EXOC6B transcript variant 2	NM_015189.2:c.	N/A	Intron Variant
EXOC6B transcript variant 7	NR_135773.1:n.	N/A	Intron Variant
EXOC6B transcript variant 8	NR_135774.1:n.	N/A	Intron Variant
EXOC6B transcript variant X1	XM_011532711.2:c.	N/A	Intron Variant
EXOC6B transcript variant X2	XM_011532712.2:c.	N/A	Intron Variant
EXOC6B transcript variant X3	XM_017003641.1:c.	N/A	Intron Variant
EXOC6B transcript variant X4	XM_005264224.1:c.	N/A	Genic Upstream Transcript Variant
EXOC6B transcript variant X5	XM_017003642.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.260	A=0.740
1000Genomes	American	Sub	694	G=0.100	A=0.900
1000Genomes	East Asian	Sub	1008	G=0.006	A=0.994
1000Genomes	Europe	Sub	1006	G=0.100	A=0.900
1000Genomes	Global	Study-wide	5008	G=0.118	A=0.882
1000Genomes	South Asian	Sub	978	G=0.070	A=0.930
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.114	A=0.886
The Genome Aggregation Database	African	Sub	8720	G=0.266	A=0.734
The Genome Aggregation Database	American	Sub	838	G=0.070	A=0.930
The Genome Aggregation Database	East Asian	Sub	1616	G=0.005	A=0.995
The Genome Aggregation Database	Europe	Sub	18470	G=0.100	A=0.899
The Genome Aggregation Database	Global	Study-wide	29946	G=0.142	A=0.857
The Genome Aggregation Database	Other	Sub	302	G=0.110	A=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.174	A=0.825
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.119	A=0.881

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
rs1446890	0.00088	alcohol dependence	20201924

eQTL of rs1446890 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 rs1446890 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 )
chr2	72752177	72752550	E067	-43180
chr2	72760541	72760608	E067	-35122
chr2	72766193	72766762	E067	-28968
chr2	72788996	72789369	E067	-6361
chr2	72789446	72789512	E067	-6218
chr2	72789544	72789687	E067	-6043
chr2	72789688	72789932	E067	-5798
chr2	72841101	72841741	E067	45371
chr2	72751308	72751467	E068	-44263
chr2	72751475	72751601	E068	-44129
chr2	72752177	72752550	E068	-43180
chr2	72765697	72766179	E068	-29551
chr2	72766193	72766762	E068	-28968
chr2	72788996	72789369	E068	-6361
chr2	72830626	72830986	E068	34896
chr2	72765697	72766179	E069	-29551
chr2	72766193	72766762	E069	-28968
chr2	72788996	72789369	E069	-6361
chr2	72789446	72789512	E069	-6218
chr2	72789544	72789687	E069	-6043
chr2	72789688	72789932	E069	-5798
chr2	72803687	72803811	E069	7957
chr2	72841101	72841741	E069	45371
chr2	72751308	72751467	E071	-44263
chr2	72752177	72752550	E071	-43180
chr2	72760541	72760608	E071	-35122
chr2	72761007	72761141	E071	-34589
chr2	72761989	72762161	E071	-33569
chr2	72765697	72766179	E071	-29551
chr2	72766193	72766762	E071	-28968
chr2	72788996	72789369	E071	-6361
chr2	72789446	72789512	E071	-6218
chr2	72789544	72789687	E071	-6043
chr2	72789688	72789932	E071	-5798
chr2	72803687	72803811	E071	7957
chr2	72803868	72804113	E071	8138
chr2	72841974	72842054	E071	46244
chr2	72751308	72751467	E072	-44263
chr2	72751475	72751601	E072	-44129
chr2	72752177	72752550	E072	-43180
chr2	72760541	72760608	E072	-35122
chr2	72761007	72761141	E072	-34589
chr2	72765697	72766179	E072	-29551
chr2	72766193	72766762	E072	-28968
chr2	72788996	72789369	E072	-6361
chr2	72789446	72789512	E072	-6218
chr2	72789544	72789687	E072	-6043
chr2	72830626	72830986	E072	34896
chr2	72841101	72841741	E072	45371
chr2	72841974	72842054	E072	46244
chr2	72766193	72766762	E073	-28968
chr2	72788996	72789369	E073	-6361
chr2	72789446	72789512	E073	-6218
chr2	72841974	72842054	E073	46244
chr2	72751308	72751467	E074	-44263
chr2	72751475	72751601	E074	-44129
chr2	72752177	72752550	E074	-43180
chr2	72765697	72766179	E074	-29551
chr2	72766193	72766762	E074	-28968
chr2	72788996	72789369	E074	-6361
chr2	72789446	72789512	E074	-6218
chr2	72789544	72789687	E074	-6043
chr2	72789688	72789932	E074	-5798
chr2	72830626	72830986	E074	34896
chr2	72841101	72841741	E074	45371
chr2	72841974	72842054	E074	46244
chr2	72774116	72774213	E081	-21517
chr2	72830626	72830986	E082	34896