SNP Detail Info-rs3814964

Organism: Homo sapiens

Alleles: G>C / G>T

Gene : Feature

NAP1L4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0350 (42107/120008,ExAC)
T=0273 (8196/29928,GnomAD)
T=0271 (7911/29118,TOPMED)
G==0250 (3001/11976,GO-ESP)
T=0385 (1929/5008,1000G)
T=0294 (1133/3854,ALSPAC)
T=0279 (1033/3708,TWINSUK)

Position: chr11:2978277 (GRCh38.p7) (11p15.4)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.2978277G>C
GRCh38.p7 chr 11	NC_000011.10:g.2978277G>T
GRCh37.p13 chr 11	NC_000011.9:g.2999507G>C
GRCh37.p13 chr 11	NC_000011.9:g.2999507G>T
GRCh38.p7 chr 11 alt locus HSCHR11_1_CTG7	NT_187585.1:g.209347T>G
GRCh38.p7 chr 11 alt locus HSCHR11_1_CTG7	NT_187585.1:g.209347T>C

Gene: NAP1L4, nucleosome assembly protein 1 like 4(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NAP1L4 transcript	NM_005969.3:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.882	T=0.118
1000Genomes	American	Sub	694	G=0.480	T=0.520
1000Genomes	East Asian	Sub	1008	G=0.299	T=0.701
1000Genomes	Europe	Sub	1006	G=0.704	T=0.296
1000Genomes	Global	Study-wide	5008	G=0.615	T=0.385
1000Genomes	South Asian	Sub	978	G=0.580	T=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.706	T=0.294
The Exome Aggregation Consortium	American	Sub	21266	G=0.607	T=0.392
The Exome Aggregation Consortium	Asian	Sub	25028	G=0.516	T=0.483
The Exome Aggregation Consortium	Europe	Sub	72818	G=0.706	T=0.293
The Exome Aggregation Consortium	Global	Study-wide	120008	G=0.649	T=0.350
The Exome Aggregation Consortium	Other	Sub	896	G=0.660	T=0.340
The Genome Aggregation Database	African	Sub	8708	G=0.838	C=0.000
The Genome Aggregation Database	American	Sub	836	G=0.470	C=0.00,
The Genome Aggregation Database	East Asian	Sub	1614	G=0.304	C=0.000
The Genome Aggregation Database	Europe	Sub	18468	G=0.722	C=0.000
The Genome Aggregation Database	Global	Study-wide	29928	G=0.726	C=0.000
The Genome Aggregation Database	Other	Sub	302	G=0.660	C=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.728	T=0.271
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.721	T=0.279

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
rs3814964	0.000074	alcohol dependence(early age of onset)	20201924
rs3814964	0.0000745	alcoholism	pha002892
rs3814964	0.00072	alcohol dependence	20201924

eQTL of rs3814964 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 rs3814964 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

rs3814964