rs775238

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

DCTN2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0014 (444/29964,GnomAD)
T=0007 (205/29118,TOPMED)
T=0006 (32/5008,1000G)
T=0012 (47/3854,ALSPAC)
T=0012 (44/3708,TWINSUK)

Position: chr12:57544298 (GRCh38.p7) (12q13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 117 Enhancers around

Promoter: 104 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.57544298C>T
GRCh37.p13 chr 12	NC_000012.11:g.57938081C>T

Gene: DCTN2, dynactin subunit 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DCTN2 transcript variant 2	NM_001261412.1:c.	N/A	Intron Variant
DCTN2 transcript variant 3	NM_001261413.1:c.	N/A	Intron Variant
DCTN2 transcript variant 1	NM_006400.4:c.	N/A	Intron Variant
DCTN2 transcript variant X3	XM_011537761.2:c.	N/A	Intron Variant
DCTN2 transcript variant X1	XR_001748556.1:n.	N/A	Intron Variant
DCTN2 transcript variant X2	XR_944481.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=1.000	T=0.000
1000Genomes	East Asian	Sub	1008	C=1.000	T=0.000
1000Genomes	Europe	Sub	1006	C=0.977	T=0.023
1000Genomes	Global	Study-wide	5008	C=0.994	T=0.006
1000Genomes	South Asian	Sub	978	C=0.990	T=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.988	T=0.012
The Genome Aggregation Database	African	Sub	8726	C=0.998	T=0.002
The Genome Aggregation Database	American	Sub	836	C=0.990	T=0.010
The Genome Aggregation Database	East Asian	Sub	1622	C=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18478	C=0.977	T=0.022
The Genome Aggregation Database	Global	Study-wide	29964	C=0.985	T=0.014
The Genome Aggregation Database	Other	Sub	302	C=0.990	T=0.010
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.993	T=0.007
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.988	T=0.012

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
rs775238	0.00059	alcohol dependence	20201924

eQTL of rs775238 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 rs775238 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 )
chr12	57910447	57911081	E067	-27000
chr12	57911093	57911330	E067	-26751
chr12	57911348	57911490	E067	-26591
chr12	57911504	57911591	E067	-26490
chr12	57918415	57919003	E067	-19078
chr12	57941538	57941615	E067	3457
chr12	57942846	57943177	E067	4765
chr12	57911093	57911330	E068	-26751
chr12	57911348	57911490	E068	-26591
chr12	57911504	57911591	E068	-26490
chr12	57919004	57919195	E068	-18886
chr12	57919198	57919312	E068	-18769
chr12	57919329	57919413	E068	-18668
chr12	57929056	57929165	E068	-8916
chr12	57929382	57929462	E068	-8619
chr12	57929508	57929639	E068	-8442
chr12	57937337	57937458	E068	-623
chr12	57937463	57937751	E068	-330
chr12	57937883	57937951	E068	-130
chr12	57938775	57938892	E068	694
chr12	57946085	57946151	E068	8004
chr12	57946312	57946362	E068	8231
chr12	57911093	57911330	E069	-26751
chr12	57911348	57911490	E069	-26591
chr12	57918415	57919003	E069	-19078
chr12	57919004	57919195	E069	-18886
chr12	57919198	57919312	E069	-18769
chr12	57937337	57937458	E069	-623
chr12	57937463	57937751	E069	-330
chr12	57937883	57937951	E069	-130
chr12	57938775	57938892	E069	694
chr12	57918415	57919003	E070	-19078
chr12	57919004	57919195	E070	-18886
chr12	57919198	57919312	E070	-18769
chr12	57919329	57919413	E070	-18668
chr12	57919497	57919547	E070	-18534
chr12	57919596	57919669	E070	-18412
chr12	57919727	57920070	E070	-18011
chr12	57920074	57920277	E070	-17804
chr12	57920377	57920427	E070	-17654
chr12	57920470	57920903	E070	-17178
chr12	57937337	57937458	E070	-623
chr12	57937463	57937751	E070	-330
chr12	57938775	57938892	E070	694
chr12	57948692	57948811	E070	10611
chr12	57948820	57948870	E070	10739
chr12	57950684	57950748	E070	12603
chr12	57986304	57986681	E070	48223
chr12	57986737	57986941	E070	48656
chr12	57987016	57987056	E070	48935
chr12	57911348	57911490	E071	-26591
chr12	57911504	57911591	E071	-26490
chr12	57937337	57937458	E071	-623
chr12	57937463	57937751	E071	-330
chr12	57937883	57937951	E071	-130
chr12	57938775	57938892	E071	694
chr12	57941538	57941615	E071	3457
chr12	57942846	57943177	E071	4765
chr12	57947093	57947283	E071	9012
chr12	57910447	57911081	E072	-27000
chr12	57911093	57911330	E072	-26751
chr12	57911348	57911490	E072	-26591
chr12	57911504	57911591	E072	-26490
chr12	57911874	57912541	E072	-25540
chr12	57937337	57937458	E072	-623
chr12	57937463	57937751	E072	-330
chr12	57937883	57937951	E072	-130
chr12	57938775	57938892	E072	694
chr12	57910447	57911081	E073	-27000
chr12	57911093	57911330	E073	-26751
chr12	57911348	57911490	E073	-26591
chr12	57911504	57911591	E073	-26490
chr12	57918415	57919003	E073	-19078
chr12	57919004	57919195	E073	-18886
chr12	57919198	57919312	E073	-18769
chr12	57919329	57919413	E073	-18668
chr12	57919497	57919547	E073	-18534
chr12	57919596	57919669	E073	-18412
chr12	57919727	57920070	E073	-18011
chr12	57920074	57920277	E073	-17804
chr12	57937337	57937458	E073	-623
chr12	57937463	57937751	E073	-330
chr12	57937883	57937951	E073	-130
chr12	57918415	57919003	E074	-19078
chr12	57918415	57919003	E081	-19078
chr12	57919004	57919195	E081	-18886
chr12	57919198	57919312	E081	-18769
chr12	57919329	57919413	E081	-18668
chr12	57919497	57919547	E081	-18534
chr12	57919596	57919669	E081	-18412
chr12	57919727	57920070	E081	-18011
chr12	57920074	57920277	E081	-17804
chr12	57938775	57938892	E081	694
chr12	57942846	57943177	E081	4765
chr12	57946312	57946362	E081	8231
chr12	57946408	57946458	E081	8327
chr12	57946495	57946547	E081	8414
chr12	57948692	57948811	E081	10611
chr12	57948820	57948870	E081	10739
chr12	57950250	57950469	E081	12169
chr12	57986304	57986681	E081	48223
chr12	57986737	57986941	E081	48656
chr12	57987016	57987056	E081	48935
chr12	57987138	57987204	E081	49057
chr12	57918415	57919003	E082	-19078
chr12	57919004	57919195	E082	-18886
chr12	57919198	57919312	E082	-18769
chr12	57919329	57919413	E082	-18668
chr12	57919497	57919547	E082	-18534
chr12	57919596	57919669	E082	-18412
chr12	57919727	57920070	E082	-18011
chr12	57937337	57937458	E082	-623
chr12	57937463	57937751	E082	-330
chr12	57937883	57937951	E082	-130
chr12	57938775	57938892	E082	694
chr12	57948692	57948811	E082	10611
chr12	57948820	57948870	E082	10739

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	57912852	57915051	E067	-23030
chr12	57939511	57941533	E067	1430
chr12	57943248	57944621	E067	5167
chr12	57944681	57944857	E067	6600
chr12	57944886	57945001	E067	6805
chr12	57945065	57945105	E067	6984
chr12	57945115	57945274	E067	7034
chr12	57945433	57945560	E067	7352
chr12	57945589	57945751	E067	7508
chr12	57945845	57945940	E067	7764
chr12	57947293	57947404	E067	9212
chr12	57984184	57986177	E067	46103
chr12	57912852	57915051	E068	-23030
chr12	57939511	57941533	E068	1430
chr12	57943248	57944621	E068	5167
chr12	57944681	57944857	E068	6600
chr12	57944886	57945001	E068	6805
chr12	57945065	57945105	E068	6984
chr12	57945115	57945274	E068	7034
chr12	57945433	57945560	E068	7352
chr12	57945589	57945751	E068	7508
chr12	57947293	57947404	E068	9212
chr12	57984184	57986177	E068	46103
chr12	57912852	57915051	E069	-23030
chr12	57939511	57941533	E069	1430
chr12	57943248	57944621	E069	5167
chr12	57944681	57944857	E069	6600
chr12	57944886	57945001	E069	6805
chr12	57945065	57945105	E069	6984
chr12	57945115	57945274	E069	7034
chr12	57945433	57945560	E069	7352
chr12	57945589	57945751	E069	7508
chr12	57945845	57945940	E069	7764
chr12	57947293	57947404	E069	9212
chr12	57984184	57986177	E069	46103
chr12	57912852	57915051	E070	-23030
chr12	57939511	57941533	E070	1430
chr12	57943248	57944621	E070	5167
chr12	57944681	57944857	E070	6600
chr12	57944886	57945001	E070	6805
chr12	57945065	57945105	E070	6984
chr12	57945115	57945274	E070	7034
chr12	57945433	57945560	E070	7352
chr12	57945589	57945751	E070	7508
chr12	57945845	57945940	E070	7764
chr12	57947293	57947404	E070	9212
chr12	57984184	57986177	E070	46103
chr12	57912852	57915051	E071	-23030
chr12	57939511	57941533	E071	1430
chr12	57943248	57944621	E071	5167
chr12	57944681	57944857	E071	6600
chr12	57984184	57986177	E071	46103
chr12	57912852	57915051	E072	-23030
chr12	57939511	57941533	E072	1430
chr12	57943248	57944621	E072	5167
chr12	57944681	57944857	E072	6600
chr12	57944886	57945001	E072	6805
chr12	57945065	57945105	E072	6984
chr12	57945115	57945274	E072	7034
chr12	57945433	57945560	E072	7352
chr12	57945589	57945751	E072	7508
chr12	57945845	57945940	E072	7764
chr12	57947293	57947404	E072	9212
chr12	57984184	57986177	E072	46103
chr12	57912852	57915051	E073	-23030
chr12	57939511	57941533	E073	1430
chr12	57943248	57944621	E073	5167
chr12	57944681	57944857	E073	6600
chr12	57944886	57945001	E073	6805
chr12	57945065	57945105	E073	6984
chr12	57945115	57945274	E073	7034
chr12	57945433	57945560	E073	7352
chr12	57945589	57945751	E073	7508
chr12	57945845	57945940	E073	7764
chr12	57947293	57947404	E073	9212
chr12	57984184	57986177	E073	46103
chr12	57912852	57915051	E074	-23030
chr12	57939511	57941533	E074	1430
chr12	57943248	57944621	E074	5167
chr12	57944681	57944857	E074	6600
chr12	57984184	57986177	E074	46103
chr12	57912852	57915051	E081	-23030
chr12	57943248	57944621	E081	5167
chr12	57944681	57944857	E081	6600
chr12	57944886	57945001	E081	6805
chr12	57945065	57945105	E081	6984
chr12	57945115	57945274	E081	7034
chr12	57945433	57945560	E081	7352
chr12	57945589	57945751	E081	7508
chr12	57945845	57945940	E081	7764
chr12	57947293	57947404	E081	9212
chr12	57984184	57986177	E081	46103
chr12	57912852	57915051	E082	-23030
chr12	57939511	57941533	E082	1430
chr12	57943248	57944621	E082	5167
chr12	57944681	57944857	E082	6600
chr12	57944886	57945001	E082	6805
chr12	57945065	57945105	E082	6984
chr12	57945115	57945274	E082	7034
chr12	57945433	57945560	E082	7352
chr12	57945589	57945751	E082	7508
chr12	57945845	57945940	E082	7764
chr12	57947293	57947404	E082	9212
chr12	57984184	57986177	E082	46103