rs9996218

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0250 (7507/29924,GnomAD)
A==0317 (9240/29118,TOPMED)
A==0280 (1401/5008,1000G)
A==0146 (562/3854,ALSPAC)
A==0141 (521/3708,TWINSUK)

Position: chr4:77829346 (GRCh38.p7) (4q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 68 Enhancers around

Promoter: 41 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.77829346A>G
GRCh37.p13 chr 4	NC_000004.11:g.78750500A>G

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.555	G=0.445
1000Genomes	American	Sub	694	A=0.130	G=0.870
1000Genomes	East Asian	Sub	1008	A=0.194	G=0.806
1000Genomes	Europe	Sub	1006	A=0.129	G=0.871
1000Genomes	Global	Study-wide	5008	A=0.280	G=0.720
1000Genomes	South Asian	Sub	978	A=0.260	G=0.740
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.146	G=0.854
The Genome Aggregation Database	African	Sub	8700	A=0.515	G=0.485
The Genome Aggregation Database	American	Sub	838	A=0.150	G=0.850
The Genome Aggregation Database	East Asian	Sub	1620	A=0.162	G=0.838
The Genome Aggregation Database	Europe	Sub	18464	A=0.140	G=0.859
The Genome Aggregation Database	Global	Study-wide	29924	A=0.250	G=0.749
The Genome Aggregation Database	Other	Sub	302	A=0.140	G=0.860
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.317	G=0.682
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.141	G=0.859

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs9996218	9.87E-05	alcohol consumption	23743675

eQTL of rs9996218 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr4:78750500	CNOT6L	ENSG00000138767.8	A>G	4.5600e-15	9731	Cerebellum
Chr4:78750500	CNOT6L	ENSG00000138767.8	A>G	7.2038e-4	9731	Frontal_Cortex_BA9
Chr4:78750500	CNOT6L	ENSG00000138767.8	A>G	3.3539e-6	9731	Cortex
Chr4:78750500	CNOT6L	ENSG00000138767.8	A>G	8.9878e-8	9731	Cerebellar_Hemisphere
Chr4:78750500	CNOT6L	ENSG00000138767.8	A>G	3.2735e-5	9731	Caudate_basal_ganglia
Chr4:78750500	CNOT6L	ENSG00000138767.8	A>G	7.4447e-4	9731	Brain_Spinal_cord_cervical
Chr4:78750500	CNOT6L	ENSG00000138767.8	A>G	8.5293e-8	9731	Putamen_basal_ganglia
Chr4:78750500	CNOT6L	ENSG00000138767.8	A>G	5.2792e-5	9731	Nucleus_accumbens_basal_ganglia

meQTL of rs9996218 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 )
chr4	78702953	78703053	E067	-47447
chr4	78703362	78703527	E067	-46973
chr4	78722035	78722202	E067	-28298
chr4	78722256	78722380	E067	-28120
chr4	78722404	78722470	E067	-28030
chr4	78722483	78722656	E067	-27844
chr4	78736625	78736683	E067	-13817
chr4	78736879	78737073	E067	-13427
chr4	78742801	78743329	E067	-7171
chr4	78743347	78743599	E067	-6901
chr4	78722035	78722202	E068	-28298
chr4	78722256	78722380	E068	-28120
chr4	78722404	78722470	E068	-28030
chr4	78722483	78722656	E068	-27844
chr4	78736625	78736683	E068	-13817
chr4	78736879	78737073	E068	-13427
chr4	78738053	78738138	E068	-12362
chr4	78742801	78743329	E068	-7171
chr4	78704448	78704571	E069	-45929
chr4	78722035	78722202	E069	-28298
chr4	78722256	78722380	E069	-28120
chr4	78722404	78722470	E069	-28030
chr4	78722483	78722656	E069	-27844
chr4	78736625	78736683	E069	-13817
chr4	78736879	78737073	E069	-13427
chr4	78742801	78743329	E069	-7171
chr4	78743347	78743599	E069	-6901
chr4	78702953	78703053	E070	-47447
chr4	78703362	78703527	E070	-46973
chr4	78704448	78704571	E070	-45929
chr4	78736625	78736683	E070	-13817
chr4	78782160	78782214	E070	31660
chr4	78782432	78782632	E070	31932
chr4	78702953	78703053	E071	-47447
chr4	78703362	78703527	E071	-46973
chr4	78711188	78711723	E071	-38777
chr4	78722035	78722202	E071	-28298
chr4	78722256	78722380	E071	-28120
chr4	78722404	78722470	E071	-28030
chr4	78722483	78722656	E071	-27844
chr4	78736625	78736683	E071	-13817
chr4	78736879	78737073	E071	-13427
chr4	78742801	78743329	E071	-7171
chr4	78782432	78782632	E071	31932
chr4	78702953	78703053	E072	-47447
chr4	78703362	78703527	E072	-46973
chr4	78718519	78718632	E072	-31868
chr4	78742801	78743329	E072	-7171
chr4	78702953	78703053	E073	-47447
chr4	78720523	78720573	E073	-29927
chr4	78736879	78737073	E073	-13427
chr4	78742801	78743329	E073	-7171
chr4	78743347	78743599	E073	-6901
chr4	78798485	78798550	E073	47985
chr4	78721744	78721795	E074	-28705
chr4	78722035	78722202	E074	-28298
chr4	78722256	78722380	E074	-28120
chr4	78722404	78722470	E074	-28030
chr4	78722483	78722656	E074	-27844
chr4	78724150	78724243	E074	-26257
chr4	78742801	78743329	E074	-7171
chr4	78782432	78782632	E074	31932
chr4	78711188	78711723	E081	-38777
chr4	78782432	78782632	E081	31932
chr4	78736625	78736683	E082	-13817
chr4	78736879	78737073	E082	-13427
chr4	78782432	78782632	E082	31932
chr4	78785259	78785299	E082	34759

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr4	78738623	78740807	E067	-9693
chr4	78740810	78742783	E067	-7717
chr4	78782671	78784705	E067	32171
chr4	78784809	78784882	E067	34309
chr4	78784918	78785151	E067	34418
chr4	78738623	78740807	E068	-9693
chr4	78740810	78742783	E068	-7717
chr4	78782671	78784705	E068	32171
chr4	78784809	78784882	E068	34309
chr4	78784918	78785151	E068	34418
chr4	78738623	78740807	E069	-9693
chr4	78740810	78742783	E069	-7717
chr4	78782671	78784705	E069	32171
chr4	78784809	78784882	E069	34309
chr4	78784918	78785151	E069	34418
chr4	78738623	78740807	E070	-9693
chr4	78740810	78742783	E070	-7717
chr4	78782671	78784705	E070	32171
chr4	78784809	78784882	E070	34309
chr4	78784918	78785151	E070	34418
chr4	78738623	78740807	E071	-9693
chr4	78740810	78742783	E071	-7717
chr4	78782671	78784705	E071	32171
chr4	78784809	78784882	E071	34309
chr4	78784918	78785151	E071	34418
chr4	78738623	78740807	E072	-9693
chr4	78740810	78742783	E072	-7717
chr4	78782671	78784705	E072	32171
chr4	78738623	78740807	E073	-9693
chr4	78740810	78742783	E073	-7717
chr4	78782671	78784705	E073	32171
chr4	78738623	78740807	E074	-9693
chr4	78740810	78742783	E074	-7717
chr4	78782671	78784705	E074	32171
chr4	78738623	78740807	E081	-9693
chr4	78782671	78784705	E081	32171
chr4	78738623	78740807	E082	-9693
chr4	78740810	78742783	E082	-7717
chr4	78782671	78784705	E082	32171
chr4	78784809	78784882	E082	34309
chr4	78784918	78785151	E082	34418