rs12471136

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

EXOC6B : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0125 (3748/29922,GnomAD)
A==0150 (4367/29116,TOPMED)
A==0100 (501/5008,1000G)
A==0111 (428/3854,ALSPAC)
A==0117 (432/3708,TWINSUK)

Position: chr2:72562188 (GRCh38.p7) (2p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 67 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.72562188A>G
GRCh37.p13 chr 2	NC_000002.11:g.72789317A>G

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 X5	XM_017003642.1:c.	N/A	Intron Variant
EXOC6B transcript variant X4	XM_005264224.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.198	G=0.802
1000Genomes	American	Sub	694	A=0.100	G=0.900
1000Genomes	East Asian	Sub	1008	A=0.006	G=0.994
1000Genomes	Europe	Sub	1006	A=0.097	G=0.903
1000Genomes	Global	Study-wide	5008	A=0.100	G=0.900
1000Genomes	South Asian	Sub	978	A=0.070	G=0.930
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.111	G=0.889
The Genome Aggregation Database	African	Sub	8712	A=0.213	G=0.787
The Genome Aggregation Database	American	Sub	836	A=0.070	G=0.930
The Genome Aggregation Database	East Asian	Sub	1620	A=0.005	G=0.995
The Genome Aggregation Database	Europe	Sub	18452	A=0.097	G=0.902
The Genome Aggregation Database	Global	Study-wide	29922	A=0.125	G=0.874
The Genome Aggregation Database	Other	Sub	302	A=0.120	G=0.880
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.150	G=0.850
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.117	G=0.883

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
rs12471136	0.0008	alcohol dependence	20201924

eQTL of rs12471136 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 rs12471136 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	72741315	72741476	E067	-47841
chr2	72752177	72752550	E067	-36767
chr2	72760541	72760608	E067	-28709
chr2	72766193	72766762	E067	-22555
chr2	72788996	72789369	E067	0
chr2	72789446	72789512	E067	129
chr2	72789544	72789687	E067	227
chr2	72789688	72789932	E067	371
chr2	72751308	72751467	E068	-37850
chr2	72751475	72751601	E068	-37716
chr2	72752177	72752550	E068	-36767
chr2	72765697	72766179	E068	-23138
chr2	72766193	72766762	E068	-22555
chr2	72788996	72789369	E068	0
chr2	72830626	72830986	E068	41309
chr2	72765697	72766179	E069	-23138
chr2	72766193	72766762	E069	-22555
chr2	72788996	72789369	E069	0
chr2	72789446	72789512	E069	129
chr2	72789544	72789687	E069	227
chr2	72789688	72789932	E069	371
chr2	72803687	72803811	E069	14370
chr2	72742864	72742982	E071	-46335
chr2	72745671	72745862	E071	-43455
chr2	72751308	72751467	E071	-37850
chr2	72752177	72752550	E071	-36767
chr2	72760541	72760608	E071	-28709
chr2	72761007	72761141	E071	-28176
chr2	72761989	72762161	E071	-27156
chr2	72765697	72766179	E071	-23138
chr2	72766193	72766762	E071	-22555
chr2	72788996	72789369	E071	0
chr2	72789446	72789512	E071	129
chr2	72789544	72789687	E071	227
chr2	72789688	72789932	E071	371
chr2	72803687	72803811	E071	14370
chr2	72803868	72804113	E071	14551
chr2	72742864	72742982	E072	-46335
chr2	72745671	72745862	E072	-43455
chr2	72751308	72751467	E072	-37850
chr2	72751475	72751601	E072	-37716
chr2	72752177	72752550	E072	-36767
chr2	72760541	72760608	E072	-28709
chr2	72761007	72761141	E072	-28176
chr2	72765697	72766179	E072	-23138
chr2	72766193	72766762	E072	-22555
chr2	72788996	72789369	E072	0
chr2	72789446	72789512	E072	129
chr2	72789544	72789687	E072	227
chr2	72830626	72830986	E072	41309
chr2	72742864	72742982	E073	-46335
chr2	72766193	72766762	E073	-22555
chr2	72788996	72789369	E073	0
chr2	72789446	72789512	E073	129
chr2	72742864	72742982	E074	-46335
chr2	72751308	72751467	E074	-37850
chr2	72751475	72751601	E074	-37716
chr2	72752177	72752550	E074	-36767
chr2	72765697	72766179	E074	-23138
chr2	72766193	72766762	E074	-22555
chr2	72788996	72789369	E074	0
chr2	72789446	72789512	E074	129
chr2	72789544	72789687	E074	227
chr2	72789688	72789932	E074	371
chr2	72830626	72830986	E074	41309
chr2	72774116	72774213	E081	-15104
chr2	72830626	72830986	E082	41309