rs11178177

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

CNOT2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0273 (8176/29932,GnomAD)
T=0270 (7865/29118,TOPMED)
T=0291 (1455/5008,1000G)
T=0285 (1098/3854,ALSPAC)
T=0269 (999/3708,TWINSUK)

Position: chr12:70297525 (GRCh38.p7) (12q15)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 105 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.70297525C>T
GRCh37.p13 chr 12	NC_000012.11:g.70691305C>T

Gene: CNOT2, CCR4-NOT transcription complex subunit 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CNOT2 transcript variant 3	NM_001199302.1:c.	N/A	Intron Variant
CNOT2 transcript variant 1	NM_001199303.1:c.	N/A	Intron Variant
CNOT2 transcript variant 2	NM_014515.5:c.	N/A	Intron Variant
CNOT2 transcript variant 4	NR_037615.1:n.	N/A	Intron Variant
CNOT2 transcript variant X3	XM_006719429.3:c.	N/A	Intron Variant
CNOT2 transcript variant X2	XM_006719430.3:c.	N/A	Intron Variant
CNOT2 transcript variant X10	XM_006719432.3:c.	N/A	Intron Variant
CNOT2 transcript variant X12	XM_006719433.3:c.	N/A	Intron Variant
CNOT2 transcript variant X1	XM_011538399.1:c.	N/A	Intron Variant
CNOT2 transcript variant X7	XM_011538400.2:c.	N/A	Intron Variant
CNOT2 transcript variant X4	XM_017019348.1:c.	N/A	Intron Variant
CNOT2 transcript variant X5	XM_017019349.1:c.	N/A	Intron Variant
CNOT2 transcript variant X6	XM_017019350.1:c.	N/A	Intron Variant
CNOT2 transcript variant X8	XM_017019351.1:c.	N/A	Intron Variant
CNOT2 transcript variant X9	XM_017019352.1:c.	N/A	Intron Variant
CNOT2 transcript variant X13	XM_017019353.1:c.	N/A	Intron Variant
CNOT2 transcript variant X15	XM_017019354.1:c.	N/A	Intron Variant
CNOT2 transcript variant X11	XR_001748718.1:n.	N/A	Intron Variant
CNOT2 transcript variant X15	XR_001748719.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.774	T=0.226
1000Genomes	American	Sub	694	C=0.520	T=0.480
1000Genomes	East Asian	Sub	1008	C=0.764	T=0.236
1000Genomes	Europe	Sub	1006	C=0.694	T=0.306
1000Genomes	Global	Study-wide	5008	C=0.709	T=0.291
1000Genomes	South Asian	Sub	978	C=0.720	T=0.280
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.715	T=0.285
The Genome Aggregation Database	African	Sub	8706	C=0.766	T=0.234
The Genome Aggregation Database	American	Sub	838	C=0.500	T=0.500
The Genome Aggregation Database	East Asian	Sub	1618	C=0.771	T=0.229
The Genome Aggregation Database	Europe	Sub	18468	C=0.715	T=0.284
The Genome Aggregation Database	Global	Study-wide	29932	C=0.726	T=0.273
The Genome Aggregation Database	Other	Sub	302	C=0.700	T=0.300
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.729	T=0.270
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.731	T=0.269

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs11178177	0.000842	alcohol dependence	21314694

eQTL of rs11178177 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 rs11178177 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	70641570	70641682	E067	-49623
chr12	70642559	70643082	E067	-48223
chr12	70648827	70648918	E067	-42387
chr12	70648934	70648995	E067	-42310
chr12	70649152	70649393	E067	-41912
chr12	70649487	70649527	E067	-41778
chr12	70649533	70649593	E067	-41712
chr12	70658004	70658054	E067	-33251
chr12	70658127	70658331	E067	-32974
chr12	70665268	70665462	E067	-25843
chr12	70665734	70665890	E067	-25415
chr12	70684042	70684148	E067	-7157
chr12	70684151	70684237	E067	-7068
chr12	70684289	70684339	E067	-6966
chr12	70702180	70702240	E067	10875
chr12	70641355	70641395	E068	-49910
chr12	70641570	70641682	E068	-49623
chr12	70642559	70643082	E068	-48223
chr12	70644656	70644720	E068	-46585
chr12	70644790	70644850	E068	-46455
chr12	70644975	70645025	E068	-46280
chr12	70645088	70645244	E068	-46061
chr12	70645300	70645374	E068	-45931
chr12	70657756	70657796	E068	-33509
chr12	70658004	70658054	E068	-33251
chr12	70658127	70658331	E068	-32974
chr12	70664818	70665133	E068	-26172
chr12	70683675	70683731	E068	-7574
chr12	70683934	70683998	E068	-7307
chr12	70684042	70684148	E068	-7157
chr12	70684151	70684237	E068	-7068
chr12	70684289	70684339	E068	-6966
chr12	70641570	70641682	E069	-49623
chr12	70642559	70643082	E069	-48223
chr12	70644975	70645025	E069	-46280
chr12	70645088	70645244	E069	-46061
chr12	70645300	70645374	E069	-45931
chr12	70645453	70645518	E069	-45787
chr12	70645574	70645657	E069	-45648
chr12	70648827	70648918	E069	-42387
chr12	70648934	70648995	E069	-42310
chr12	70649152	70649393	E069	-41912
chr12	70652375	70653020	E069	-38285
chr12	70657756	70657796	E069	-33509
chr12	70658004	70658054	E069	-33251
chr12	70658127	70658331	E069	-32974
chr12	70661105	70661155	E069	-30150
chr12	70661187	70661822	E069	-29483
chr12	70662150	70662262	E069	-29043
chr12	70680394	70680494	E069	-10811
chr12	70646650	70647018	E070	-44287
chr12	70647084	70647281	E070	-44024
chr12	70641355	70641395	E071	-49910
chr12	70642559	70643082	E071	-48223
chr12	70643808	70643947	E071	-47358
chr12	70648827	70648918	E071	-42387
chr12	70648934	70648995	E071	-42310
chr12	70649152	70649393	E071	-41912
chr12	70661105	70661155	E071	-30150
chr12	70661187	70661822	E071	-29483
chr12	70662150	70662262	E071	-29043
chr12	70664590	70664807	E071	-26498
chr12	70664818	70665133	E071	-26172
chr12	70671903	70672028	E071	-19277
chr12	70683345	70683427	E071	-7878
chr12	70683675	70683731	E071	-7574
chr12	70683934	70683998	E071	-7307
chr12	70684042	70684148	E071	-7157
chr12	70684151	70684237	E071	-7068
chr12	70684289	70684339	E071	-6966
chr12	70702180	70702240	E071	10875
chr12	70702364	70702442	E071	11059
chr12	70641355	70641395	E072	-49910
chr12	70649152	70649393	E072	-41912
chr12	70661187	70661822	E072	-29483
chr12	70664590	70664807	E072	-26498
chr12	70664818	70665133	E072	-26172
chr12	70666041	70666268	E072	-25037
chr12	70666436	70666600	E072	-24705
chr12	70680394	70680494	E072	-10811
chr12	70641355	70641395	E073	-49910
chr12	70641570	70641682	E073	-49623
chr12	70648827	70648918	E073	-42387
chr12	70648934	70648995	E073	-42310
chr12	70649152	70649393	E073	-41912
chr12	70641570	70641682	E074	-49623
chr12	70642559	70643082	E074	-48223
chr12	70648827	70648918	E074	-42387
chr12	70648934	70648995	E074	-42310
chr12	70649152	70649393	E074	-41912
chr12	70649487	70649527	E074	-41778
chr12	70649533	70649593	E074	-41712
chr12	70657756	70657796	E074	-33509
chr12	70665734	70665890	E074	-25415
chr12	70666041	70666268	E074	-25037
chr12	70666436	70666600	E074	-24705
chr12	70680394	70680494	E074	-10811
chr12	70683345	70683427	E074	-7878
chr12	70683675	70683731	E074	-7574
chr12	70683934	70683998	E074	-7307
chr12	70684042	70684148	E074	-7157
chr12	70684151	70684237	E074	-7068
chr12	70684289	70684339	E074	-6966
chr12	70728676	70728824	E074	37371
chr12	70728856	70728951	E074	37551