rs7590720

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PECR : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0273 (8171/29924,GnomAD)
G==0293 (8547/29118,TOPMED)
G==0284 (1422/5008,1000G)
G==0298 (1148/3854,ALSPAC)
G==0287 (1064/3708,TWINSUK)

Position: chr2:216033935 (GRCh38.p7) (2q35)

Phenotype: AD

Dataset:

GWASdb2 | GWASCatalog

Publications: 10 publication(s)

Genomic View: See rs on genome

Enhancer: 37 Enhancers around

Promoter: 20 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.216033935G>A
GRCh37.p13 chr 2	NC_000002.11:g.216898658G>A

Molecule type	Change	Amino acid[Codon]	SO Term
PECR transcript	NM_018441.5:c.	N/A	Genic Downstream Transcript Variant
PECR transcript variant X4	XM_011511478.2:c.	N/A	Genic Downstream Transcript Variant
PECR transcript variant X1	XR_001738847.1:n.	N/A	Intron Variant
PECR transcript variant X2	XR_001738848.1:n.	N/A	Genic Downstream Transcript Variant
PECR transcript variant X3	XR_001738849.1:n.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.219	A=0.781
1000Genomes	American	Sub	694	G=0.210	A=0.790
1000Genomes	East Asian	Sub	1008	G=0.318	A=0.682
1000Genomes	Europe	Sub	1006	G=0.284	A=0.716
1000Genomes	Global	Study-wide	5008	G=0.284	A=0.716
1000Genomes	South Asian	Sub	978	G=0.390	A=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.298	A=0.702
The Genome Aggregation Database	African	Sub	8708	G=0.230	A=0.770
The Genome Aggregation Database	American	Sub	838	G=0.200	A=0.800
The Genome Aggregation Database	East Asian	Sub	1618	G=0.303	A=0.697
The Genome Aggregation Database	Europe	Sub	18458	G=0.292	A=0.707
The Genome Aggregation Database	Global	Study-wide	29924	G=0.273	A=0.726
The Genome Aggregation Database	Other	Sub	302	G=0.370	A=0.630
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.293	A=0.706
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.287	A=0.713

PMID	Title	Author	Journal
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry
22281715	Recent advances in the genetic epidemiology and molecular genetics of substance use disorders.	Kendler KS	Nat Neurosci
22384374	Glypican Gene GPC5 Participates in the Behavioral Response to Ethanol: Evidence from Humans, Mice, and Fruit Flies.	Joslyn G	G3 (Bethesda)
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res
21438146	Dysfunctional gene splicing as a potential contributor to neuropsychiatric disorders.	Glatt SJ	Am J Med Genet B Neuropsychiatr Genet
21471458	Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption.	Schumann G	Proc Natl Acad Sci U S A
20202923	A genome-wide association study of alcohol dependence.	Bierut LJ	Proc Natl Acad Sci U S A
25043041	Neuropsychosocial profiles of current and future adolescent alcohol misusers.	Whelan R	Nature
21876473	Confirmation of prior evidence of genetic susceptibility to alcoholism in a genome-wide association study of comorbid alcoholism and bipolar disorder.	Lydall GJ	Psychiatr Genet
21858135	Efficient replication of over 180 genetic associations with self-reported medical data.	Tung JY	PLoS One

SNP ID	p-value	Traits	Study
rs7590720	1E-08	alcohol dependence	19581569

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
cg12620499	chr2:216877984	MREG	-0.0135551069924102	3.8262e-20

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	216863175	216864003	E067	-34655
chr2	216863175	216864003	E068	-34655
chr2	216896711	216897035	E068	-1623
chr2	216897191	216897259	E068	-1399
chr2	216897639	216897744	E068	-914
chr2	216898385	216898439	E068	-219
chr2	216898469	216898525	E068	-133
chr2	216898666	216899155	E068	8
chr2	216947657	216947835	E068	48999
chr2	216948066	216948106	E068	49408
chr2	216863175	216864003	E069	-34655
chr2	216897191	216897259	E070	-1399
chr2	216863175	216864003	E071	-34655
chr2	216866717	216866864	E071	-31794
chr2	216866900	216867004	E071	-31654
chr2	216867076	216867346	E071	-31312
chr2	216878765	216878940	E071	-19718
chr2	216948066	216948106	E071	49408
chr2	216863175	216864003	E072	-34655
chr2	216865826	216865898	E072	-32760
chr2	216878765	216878940	E072	-19718
chr2	216948066	216948106	E072	49408
chr2	216859442	216859505	E073	-39153
chr2	216896711	216897035	E073	-1623
chr2	216897191	216897259	E073	-1399
chr2	216863175	216864003	E074	-34655
chr2	216878765	216878940	E074	-19718
chr2	216947657	216947835	E074	48999
chr2	216948066	216948106	E074	49408
chr2	216878765	216878940	E081	-19718
chr2	216935916	216936139	E081	37258
chr2	216936253	216936312	E081	37595
chr2	216936385	216936435	E081	37727
chr2	216948066	216948106	E081	49408
chr2	216868868	216868965	E082	-29693
chr2	216935396	216935478	E082	36738
chr2	216935916	216936139	E082	37258

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	216876822	216878657	E067	-20001
chr2	216946052	216947441	E067	47394
chr2	216876822	216878657	E068	-20001
chr2	216946052	216947441	E068	47394
chr2	216876822	216878657	E069	-20001
chr2	216946052	216947441	E069	47394
chr2	216876822	216878657	E070	-20001
chr2	216946052	216947441	E070	47394
chr2	216876822	216878657	E071	-20001
chr2	216946052	216947441	E071	47394
chr2	216876822	216878657	E072	-20001
chr2	216946052	216947441	E072	47394
chr2	216876822	216878657	E073	-20001
chr2	216946052	216947441	E073	47394
chr2	216876822	216878657	E074	-20001
chr2	216946052	216947441	E074	47394
chr2	216876822	216878657	E081	-20001
chr2	216946052	216947441	E081	47394
chr2	216876822	216878657	E082	-20001
chr2	216946052	216947441	E082	47394