rs416391

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

CSMD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0083 (2497/29964,GnomAD)
T=0101 (2960/29118,TOPMED)
T=0100 (500/5008,1000G)
T=0061 (236/3854,ALSPAC)
T=0064 (239/3708,TWINSUK)

Position: chr1:33582668 (GRCh38.p7) (1p35.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 2 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.33582668C>T
GRCh37.p13 chr 1	NC_000001.10:g.34048268C>T

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 X10	XM_017000194.1:c.	N/A	Intron Variant
CSMD2 transcript variant X8	XM_017000192.1:c.	N/A	Genic Downstream Transcript Variant
CSMD2 transcript variant X9	XM_017000193.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.852	T=0.148
1000Genomes	American	Sub	694	C=0.940	T=0.060
1000Genomes	East Asian	Sub	1008	C=0.975	T=0.025
1000Genomes	Europe	Sub	1006	C=0.936	T=0.064
1000Genomes	Global	Study-wide	5008	C=0.900	T=0.100
1000Genomes	South Asian	Sub	978	C=0.820	T=0.180
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.939	T=0.061
The Genome Aggregation Database	African	Sub	8714	C=0.850	T=0.150
The Genome Aggregation Database	American	Sub	838	C=0.960	T=0.040
The Genome Aggregation Database	East Asian	Sub	1622	C=0.983	T=0.017
The Genome Aggregation Database	Europe	Sub	18488	C=0.940	T=0.059
The Genome Aggregation Database	Global	Study-wide	29964	C=0.916	T=0.083
The Genome Aggregation Database	Other	Sub	302	C=0.900	T=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.898	T=0.101
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.936	T=0.064

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
rs416391	0.0000399	alcoholism	pha002892
rs416391	0.00004	Alcohol dependence (early age of onset)	20201924
rs416391	0.00034	alcohol dependence	20201924

eQTL of rs416391 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 rs416391 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	34081265	34081511	E070	32997
chr1	34038209	34038312	E081	-9956