rs2826660

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

NCAM2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0182 (5464/29884,GnomAD)
G=0167 (4868/29118,TOPMED)
G=0129 (645/5008,1000G)
G=0220 (849/3854,ALSPAC)
G=0231 (858/3708,TWINSUK)

Position: chr21:21116096 (GRCh38.p7) (21q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 21	NC_000021.9:g.21116096A>G
GRCh38.p7 chr 21	NC_000021.9:g.21116096A>T
GRCh37.p13 chr 21	NC_000021.8:g.22488414A>G
GRCh37.p13 chr 21	NC_000021.8:g.22488414A>T

Gene: NCAM2, neural cell adhesion molecule 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NCAM2 transcript	NM_004540.3:c.	N/A	Intron Variant
NCAM2 transcript variant X2	XM_011529576.2:c.	N/A	Intron Variant
NCAM2 transcript variant X4	XM_011529579.2:c.	N/A	Intron Variant
NCAM2 transcript variant X3	XM_017028353.1:c.	N/A	Intron Variant
NCAM2 transcript variant X7	XM_017028354.1:c.	N/A	Intron Variant
NCAM2 transcript variant X9	XM_017028355.1:c.	N/A	Intron Variant
NCAM2 transcript variant X10	XM_017028356.1:c.	N/A	Intron Variant
NCAM2 transcript variant X12	XM_017028357.1:c.	N/A	Intron Variant
NCAM2 transcript variant X1	XM_011529575.2:c.	N/A	Genic Upstream Transcript Variant
NCAM2 transcript variant X5	XM_011529580.2:c.	N/A	Genic Upstream Transcript Variant
NCAM2 transcript variant X6	XM_011529581.2:c.	N/A	Genic Upstream Transcript Variant
NCAM2 transcript variant X8	XM_011529582.2:c.	N/A	Genic Upstream Transcript Variant
NCAM2 transcript variant X11	XM_011529585.2:c.	N/A	Genic Upstream Transcript Variant
NCAM2 transcript variant X13	XM_017028358.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.881	G=0.119
1000Genomes	American	Sub	694	A=0.840	G=0.160
1000Genomes	East Asian	Sub	1008	A=0.991	G=0.009
1000Genomes	Europe	Sub	1006	A=0.760	G=0.240
1000Genomes	Global	Study-wide	5008	A=0.871	G=0.129
1000Genomes	South Asian	Sub	978	A=0.870	G=0.130
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.780	G=0.220
The Genome Aggregation Database	African	Sub	8702	A=0.869	G=0.131
The Genome Aggregation Database	American	Sub	834	A=0.860	G=0.14,
The Genome Aggregation Database	East Asian	Sub	1620	A=0.993	G=0.007
The Genome Aggregation Database	Europe	Sub	18426	A=0.775	G=0.224
The Genome Aggregation Database	Global	Study-wide	29884	A=0.817	G=0.182
The Genome Aggregation Database	Other	Sub	302	A=0.760	G=0.24,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.832	G=0.167
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.769	G=0.231

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs2826660	6.52E-06	alcohol dependence (age at onset)	24962325

eQTL of rs2826660 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 rs2826660 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.