SNP Detail Info-rs7533254

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CSMD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0027 (809/29984,GnomAD)
A=0038 (1122/29118,TOPMED)
A=0026 (132/5008,1000G)
A=0000 (0/3854,ALSPAC)
A=0001 (2/3708,TWINSUK)

Position: chr1:33716230 (GRCh38.p7) (1p35.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 50 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.33716230G>A
GRCh37.p13 chr 1	NC_000001.10:g.34181830G>A

Gene: CSMD2, CUB and Sushi multiple domains 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CSMD2 transcript variant 1	NM_001281956.1:c.	N/A	Intron Variant
CSMD2 transcript variant 2	NM_052896.4:c.	N/A	Intron Variant
CSMD2 transcript variant X1	XM_017000185.1:c.	N/A	Intron Variant
CSMD2 transcript variant X2	XM_017000186.1:c.	N/A	Intron Variant
CSMD2 transcript variant X3	XM_017000187.1:c.	N/A	Intron Variant
CSMD2 transcript variant X4	XM_017000188.1:c.	N/A	Intron Variant
CSMD2 transcript variant X5	XM_017000189.1:c.	N/A	Intron Variant
CSMD2 transcript variant X6	XM_017000190.1:c.	N/A	Intron Variant
CSMD2 transcript variant X7	XM_017000191.1:c.	N/A	Intron Variant
CSMD2 transcript variant X8	XM_017000192.1:c.	N/A	Intron Variant
CSMD2 transcript variant X9	XM_017000193.1:c.	N/A	Intron Variant
CSMD2 transcript variant X10	XM_017000194.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.907	A=0.093
1000Genomes	American	Sub	694	G=0.990	A=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=0.999	A=0.001
1000Genomes	Global	Study-wide	5008	G=0.974	A=0.026
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=1.000	A=0.000
The Genome Aggregation Database	African	Sub	8724	G=0.909	A=0.091
The Genome Aggregation Database	American	Sub	838	G=0.990	A=0.010
The Genome Aggregation Database	East Asian	Sub	1620	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18500	G=0.999	A=0.000
The Genome Aggregation Database	Global	Study-wide	29984	G=0.973	A=0.027
The Genome Aggregation Database	Other	Sub	302	G=1.000	A=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.961	A=0.038
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.999	A=0.001

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs7533254	0.000945	alcohol dependence	21314694

eQTL of rs7533254 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 rs7533254 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 )
chr1	34150086	34150140	E068	-31690
chr1	34149582	34149708	E069	-32122
chr1	34150086	34150140	E069	-31690
chr1	34167066	34167245	E069	-14585
chr1	34201372	34201547	E070	19542
chr1	34149582	34149708	E071	-32122
chr1	34150086	34150140	E071	-31690
chr1	34166861	34166976	E071	-14854
chr1	34167066	34167245	E071	-14585
chr1	34185787	34185910	E071	3957
chr1	34185927	34185977	E071	4097
chr1	34144510	34144668	E072	-37162
chr1	34149582	34149708	E072	-32122
chr1	34150086	34150140	E072	-31690
chr1	34149582	34149708	E074	-32122
chr1	34167066	34167245	E074	-14585
chr1	34149582	34149708	E081	-32122
chr1	34150086	34150140	E081	-31690
chr1	34150489	34150789	E081	-31041
chr1	34150995	34151193	E081	-30637
chr1	34151211	34151333	E081	-30497
chr1	34151398	34151649	E081	-30181
chr1	34175502	34175622	E081	-6208
chr1	34176032	34176342	E081	-5488
chr1	34176648	34176841	E081	-4989
chr1	34177164	34177225	E081	-4605
chr1	34177660	34177720	E081	-4110
chr1	34185787	34185910	E081	3957
chr1	34185927	34185977	E081	4097
chr1	34191313	34191372	E081	9483
chr1	34191516	34191694	E081	9686
chr1	34204028	34204251	E081	22198
chr1	34204361	34204434	E081	22531
chr1	34228115	34228363	E081	46285
chr1	34228452	34228502	E081	46622
chr1	34149582	34149708	E082	-32122
chr1	34150086	34150140	E082	-31690
chr1	34150489	34150789	E082	-31041
chr1	34151211	34151333	E082	-30497
chr1	34151398	34151649	E082	-30181
chr1	34164058	34164204	E082	-17626
chr1	34166861	34166976	E082	-14854
chr1	34176032	34176342	E082	-5488
chr1	34176648	34176841	E082	-4989
chr1	34177164	34177225	E082	-4605
chr1	34177660	34177720	E082	-4110
chr1	34185787	34185910	E082	3957
chr1	34185927	34185977	E082	4097
chr1	34204028	34204251	E082	22198
chr1	34204361	34204434	E082	22531

rs7533254