rs7522616

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ASAP3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0347 (10409/29938,GnomAD)
A==0435 (12693/29118,TOPMED)
A==0451 (2257/5008,1000G)
A==0172 (664/3854,ALSPAC)
A==0177 (655/3708,TWINSUK)

Position: chr1:23468421 (GRCh38.p7) (1p36.12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 58 Enhancers around

Promoter: 16 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.23468421A>G
GRCh37.p13 chr 1	NC_000001.10:g.23794914A>G

Gene: ASAP3, ArfGAP with SH3 domain, ankyrin repeat and PH domain 3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ASAP3 transcript variant 2	NM_001143778.1:c.	N/A	Intron Variant
ASAP3 transcript variant 1	NM_017707.3:c.	N/A	Intron Variant
ASAP3 transcript variant X1	XM_011541755.1:c.	N/A	Intron Variant
ASAP3 transcript variant X2	XM_017001685.1:c.	N/A	Intron Variant
ASAP3 transcript variant X3	XM_017001686.1:c.	N/A	Intron Variant
ASAP3 transcript variant X4	XM_017001687.1:c.	N/A	Intron Variant
ASAP3 transcript variant X5	XM_017001688.1:c.	N/A	Intron Variant
ASAP3 transcript variant X6	XM_017001689.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.832	G=0.168
1000Genomes	American	Sub	694	A=0.290	G=0.710
1000Genomes	East Asian	Sub	1008	A=0.362	G=0.638
1000Genomes	Europe	Sub	1006	A=0.166	G=0.834
1000Genomes	Global	Study-wide	5008	A=0.451	G=0.549
1000Genomes	South Asian	Sub	978	A=0.430	G=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.172	G=0.828
The Genome Aggregation Database	African	Sub	8706	A=0.742	G=0.258
The Genome Aggregation Database	American	Sub	838	A=0.220	G=0.780
The Genome Aggregation Database	East Asian	Sub	1612	A=0.333	G=0.667
The Genome Aggregation Database	Europe	Sub	18480	A=0.172	G=0.827
The Genome Aggregation Database	Global	Study-wide	29938	A=0.347	G=0.652
The Genome Aggregation Database	Other	Sub	302	A=0.130	G=0.870
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.435	G=0.564
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.177	G=0.823

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs7522616	6.3E-05	alcohol dependence	21703634

eQTL of rs7522616 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:23794914	TCEA3	ENSG00000204219.5	A>G	5.6995e-7	43681	Hippocampus

meQTL of rs7522616 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 )
chr1	23776437	23776886	E067	-18028
chr1	23777091	23777223	E067	-17691
chr1	23777398	23777481	E067	-17433
chr1	23777527	23777621	E067	-17293
chr1	23777734	23777778	E067	-17136
chr1	23778171	23778340	E067	-16574
chr1	23778391	23778456	E067	-16458
chr1	23792853	23792960	E067	-1954
chr1	23793011	23793244	E067	-1670
chr1	23801505	23802417	E067	6591
chr1	23811755	23811841	E067	16841
chr1	23748294	23749411	E068	-45503
chr1	23792853	23792960	E068	-1954
chr1	23793011	23793244	E068	-1670
chr1	23796631	23796814	E068	1717
chr1	23797100	23797610	E068	2186
chr1	23797718	23797824	E068	2804
chr1	23801505	23802417	E068	6591
chr1	23805366	23805891	E068	10452
chr1	23805922	23805981	E068	11008
chr1	23748294	23749411	E069	-45503
chr1	23773278	23773582	E069	-21332
chr1	23792853	23792960	E069	-1954
chr1	23793011	23793244	E069	-1670
chr1	23797100	23797610	E069	2186
chr1	23801505	23802417	E069	6591
chr1	23748294	23749411	E070	-45503
chr1	23779335	23779398	E070	-15516
chr1	23747882	23748124	E071	-46790
chr1	23748185	23748264	E071	-46650
chr1	23748294	23749411	E071	-45503
chr1	23773278	23773582	E071	-21332
chr1	23776437	23776886	E071	-18028
chr1	23792853	23792960	E071	-1954
chr1	23793011	23793244	E071	-1670
chr1	23794528	23794632	E071	-282
chr1	23801505	23802417	E071	6591
chr1	23748294	23749411	E072	-45503
chr1	23773278	23773582	E072	-21332
chr1	23776437	23776886	E072	-18028
chr1	23792853	23792960	E072	-1954
chr1	23793011	23793244	E072	-1670
chr1	23801505	23802417	E072	6591
chr1	23805366	23805891	E072	10452
chr1	23805922	23805981	E072	11008
chr1	23748294	23749411	E073	-45503
chr1	23792853	23792960	E073	-1954
chr1	23793011	23793244	E073	-1670
chr1	23797718	23797824	E073	2804
chr1	23801505	23802417	E073	6591
chr1	23809051	23809156	E073	14137
chr1	23748294	23749411	E074	-45503
chr1	23776437	23776886	E074	-18028
chr1	23792853	23792960	E074	-1954
chr1	23793011	23793244	E074	-1670
chr1	23808736	23808789	E074	13822
chr1	23808857	23808982	E074	13943
chr1	23804542	23804622	E082	9628

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	23809360	23809429	E067	14446
chr1	23809470	23811731	E067	14556
chr1	23749448	23751939	E068	-42975
chr1	23809360	23809429	E068	14446
chr1	23809470	23811731	E068	14556
chr1	23809360	23809429	E069	14446
chr1	23809470	23811731	E069	14556
chr1	23809360	23809429	E070	14446
chr1	23809470	23811731	E070	14556
chr1	23809470	23811731	E071	14556
chr1	23749448	23751939	E072	-42975
chr1	23809470	23811731	E072	14556
chr1	23809470	23811731	E073	14556
chr1	23809470	23811731	E074	14556
chr1	23809360	23809429	E082	14446
chr1	23809470	23811731	E082	14556