rs2353203

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CPAMD8 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0476 (14240/29896,GnomAD)
G==0435 (12687/29118,TOPMED)
G==0445 (2227/5008,1000G)
A=0453 (1746/3854,ALSPAC)
A=0459 (1703/3708,TWINSUK)

Position: chr19:16989170 (GRCh38.p7) (19p13.11)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 51 Enhancers around

Promoter: 5 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.16989170G>A
GRCh37.p13 chr 19	NC_000019.9:g.17099980G>A

Gene: CPAMD8, C3 and PZP like, alpha-2-macroglobulin domain containing 8(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CPAMD8 transcript	NM_015692.2:c.	N/A	Intron Variant
CPAMD8 transcript variant X1	XM_011527917.1:c.	N/A	Intron Variant
CPAMD8 transcript variant X2	XM_011527918.1:c.	N/A	Intron Variant
CPAMD8 transcript variant X3	XM_011527919.1:c.	N/A	Intron Variant
CPAMD8 transcript variant X4	XM_011527920.2:c.	N/A	Intron Variant
CPAMD8 transcript variant X7	XM_011527921.2:c.	N/A	Intron Variant
CPAMD8 transcript variant X8	XM_011527922.1:c.	N/A	Intron Variant
CPAMD8 transcript variant X9	XM_011527923.1:c.	N/A	Intron Variant
CPAMD8 transcript variant X6	XM_011527924.2:c.	N/A	Intron Variant
CPAMD8 transcript variant X5	XM_017026594.1:c.	N/A	Intron Variant
CPAMD8 transcript variant X10	XM_011527925.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.278	A=0.722
1000Genomes	American	Sub	694	G=0.540	A=0.460
1000Genomes	East Asian	Sub	1008	G=0.386	A=0.614
1000Genomes	Europe	Sub	1006	G=0.497	A=0.503
1000Genomes	Global	Study-wide	5008	G=0.445	A=0.555
1000Genomes	South Asian	Sub	978	G=0.610	A=0.390
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.547	A=0.453
The Genome Aggregation Database	African	Sub	8704	G=0.309	A=0.691
The Genome Aggregation Database	American	Sub	838	G=0.560	A=0.440
The Genome Aggregation Database	East Asian	Sub	1594	G=0.391	A=0.609
The Genome Aggregation Database	Europe	Sub	18458	G=0.559	A=0.440
The Genome Aggregation Database	Global	Study-wide	29896	G=0.476	A=0.523
The Genome Aggregation Database	Other	Sub	302	G=0.420	A=0.580
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.435	A=0.564
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.541	A=0.459

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
rs2353203	0.00038	alcohol dependence	20201924

eQTL of rs2353203 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 rs2353203 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 )
chr19	17055275	17055835	E067	-44145
chr19	17055990	17056095	E067	-43885
chr19	17056243	17056357	E067	-43623
chr19	17056360	17056454	E067	-43526
chr19	17055275	17055835	E068	-44145
chr19	17055990	17056095	E068	-43885
chr19	17131226	17131322	E068	31246
chr19	17131391	17131484	E068	31411
chr19	17131509	17131576	E068	31529
chr19	17131768	17131963	E068	31788
chr19	17054936	17055068	E069	-44912
chr19	17055275	17055835	E069	-44145
chr19	17055990	17056095	E069	-43885
chr19	17056243	17056357	E069	-43623
chr19	17056360	17056454	E069	-43526
chr19	17056562	17056675	E069	-43305
chr19	17149116	17149180	E069	49136
chr19	17054936	17055068	E071	-44912
chr19	17055275	17055835	E071	-44145
chr19	17055990	17056095	E071	-43885
chr19	17056243	17056357	E071	-43623
chr19	17056360	17056454	E071	-43526
chr19	17056562	17056675	E071	-43305
chr19	17131226	17131322	E071	31246
chr19	17131391	17131484	E071	31411
chr19	17131509	17131576	E071	31529
chr19	17055275	17055835	E072	-44145
chr19	17055990	17056095	E072	-43885
chr19	17056243	17056357	E072	-43623
chr19	17056360	17056454	E072	-43526
chr19	17131226	17131322	E072	31246
chr19	17131391	17131484	E072	31411
chr19	17131509	17131576	E072	31529
chr19	17055990	17056095	E073	-43885
chr19	17056243	17056357	E073	-43623
chr19	17056360	17056454	E073	-43526
chr19	17131391	17131484	E073	31411
chr19	17131509	17131576	E073	31529
chr19	17131768	17131963	E073	31788
chr19	17054787	17054867	E074	-45113
chr19	17054936	17055068	E074	-44912
chr19	17055275	17055835	E074	-44145
chr19	17055990	17056095	E074	-43885
chr19	17056243	17056357	E074	-43623
chr19	17056360	17056454	E074	-43526
chr19	17056562	17056675	E074	-43305
chr19	17131226	17131322	E074	31246
chr19	17131391	17131484	E074	31411
chr19	17131509	17131576	E074	31529
chr19	17131768	17131963	E074	31788
chr19	17132012	17132062	E074	32032

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	17136684	17137412	E070	36704
chr19	17136684	17137412	E071	36704
chr19	17136684	17137412	E074	36704
chr19	17136684	17137412	E082	36704
chr19	17137633	17138340	E082	37653