SNP Detail Info-rs16858596

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ARHGAP15 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0042 (1270/29980,GnomAD)
A=0027 (800/29118,TOPMED)
A=0033 (163/5008,1000G)
A=0052 (201/3854,ALSPAC)
A=0047 (175/3708,TWINSUK)

Position: chr2:143132712 (GRCh38.p7) (2q22.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 49 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.143132712G>A
GRCh37.p13 chr 2	NC_000002.11:g.143890281G>A

Gene: ARHGAP15, Rho GTPase activating protein 15(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARHGAP15 transcript	NM_018460.3:c.	N/A	Intron Variant
ARHGAP15 transcript variant X1	XM_011511479.2:c.	N/A	Intron Variant
ARHGAP15 transcript variant X4	XM_011511481.2:c.	N/A	Intron Variant
ARHGAP15 transcript variant X6	XM_011511482.2:c.	N/A	Intron Variant
ARHGAP15 transcript variant X8	XM_011511484.1:c.	N/A	Intron Variant
ARHGAP15 transcript variant X2	XM_017004499.1:c.	N/A	Intron Variant
ARHGAP15 transcript variant X5	XM_017004500.1:c.	N/A	Intron Variant
ARHGAP15 transcript variant X9	XM_017004501.1:c.	N/A	Intron Variant
ARHGAP15 transcript variant X7	XM_011511483.1:c.	N/A	Genic Upstream Transcript Variant
ARHGAP15 transcript variant X3	XR_001738850.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.986	A=0.014
1000Genomes	American	Sub	694	G=0.970	A=0.030
1000Genomes	East Asian	Sub	1008	G=0.979	A=0.021
1000Genomes	Europe	Sub	1006	G=0.935	A=0.065
1000Genomes	Global	Study-wide	5008	G=0.967	A=0.033
1000Genomes	South Asian	Sub	978	G=0.960	A=0.040
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.948	A=0.052
The Genome Aggregation Database	African	Sub	8724	G=0.985	A=0.015
The Genome Aggregation Database	American	Sub	838	G=0.980	A=0.020
The Genome Aggregation Database	East Asian	Sub	1620	G=0.977	A=0.023
The Genome Aggregation Database	Europe	Sub	18496	G=0.941	A=0.058
The Genome Aggregation Database	Global	Study-wide	29980	G=0.957	A=0.042
The Genome Aggregation Database	Other	Sub	302	G=0.980	A=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.972	A=0.027
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.953	A=0.047

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
rs16858596	0.00053	alcohol dependence	20201924

eQTL of rs16858596 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 rs16858596 in Fetal Brain

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	143919827	143920158	E067	29546
chr2	143919827	143920158	E068	29546
chr2	143914580	143914648	E070	24299
chr2	143914717	143914850	E070	24436
chr2	143914897	143914953	E070	24616
chr2	143915030	143915520	E070	24749
chr2	143915578	143915679	E070	25297
chr2	143915793	143915897	E070	25512
chr2	143915898	143915988	E070	25617
chr2	143916155	143916437	E070	25874
chr2	143916557	143916738	E070	26276
chr2	143916820	143917507	E070	26539
chr2	143918453	143918564	E070	28172
chr2	143918714	143918967	E070	28433
chr2	143919155	143919213	E070	28874
chr2	143919531	143919607	E070	29250
chr2	143919827	143920158	E070	29546
chr2	143919827	143920158	E074	29546
chr2	143913151	143913201	E081	22870
chr2	143913392	143913605	E081	23111
chr2	143914580	143914648	E081	24299
chr2	143914717	143914850	E081	24436
chr2	143914897	143914953	E081	24616
chr2	143915030	143915520	E081	24749
chr2	143915578	143915679	E081	25297
chr2	143915793	143915897	E081	25512
chr2	143915898	143915988	E081	25617
chr2	143916155	143916437	E081	25874
chr2	143916557	143916738	E081	26276
chr2	143916820	143917507	E081	26539
chr2	143917543	143917666	E081	27262
chr2	143918453	143918564	E081	28172
chr2	143918714	143918967	E081	28433
chr2	143919155	143919213	E081	28874
chr2	143919531	143919607	E081	29250
chr2	143919827	143920158	E081	29546
chr2	143920771	143920842	E081	30490
chr2	143914580	143914648	E082	24299
chr2	143914717	143914850	E082	24436
chr2	143914897	143914953	E082	24616
chr2	143916155	143916437	E082	25874
chr2	143916557	143916738	E082	26276
chr2	143916820	143917507	E082	26539
chr2	143917543	143917666	E082	27262
chr2	143918714	143918967	E082	28433
chr2	143919155	143919213	E082	28874
chr2	143919531	143919607	E082	29250
chr2	143919827	143920158	E082	29546
chr2	143920771	143920842	E082	30490

rs16858596