rs7769970

Organism: Homo sapiens

Alleles: C>G / C>T

Gene : Feature

CPNE5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0118 (3542/29980,GnomAD)
G=0134 (670/5008,1000G)
G=0044 (170/3854,ALSPAC)
G=0040 (147/3708,TWINSUK)

Position: chr6:36767703 (GRCh38.p7) (6p21.2)

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 6	NC_000006.12:g.36767703C>G
GRCh38.p7 chr 6	NC_000006.12:g.36767703C>T
GRCh37.p13 chr 6	NC_000006.11:g.36735480C>G
GRCh37.p13 chr 6	NC_000006.11:g.36735480C>T

Gene: CPNE5, copine 5(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CPNE5 transcript variant 1	NM_020939.1:c.	N/A	Intron Variant
CPNE5 transcript variant 3	NM_001314018.1:c.	N/A	Genic Upstream Transcript Variant
CPNE5 transcript variant 4	NM_001314019.1:c.	N/A	Genic Upstream Transcript Variant
CPNE5 transcript variant 5	NM_001314020.1:c.	N/A	Genic Upstream Transcript Variant
CPNE5 transcript variant 2	NM_001314017.1:c.	N/A	Genic Downstream Transcript Variant
CPNE5 transcript variant X5	XM_005249247.2:c.	N/A	Intron Variant
CPNE5 transcript variant X1	XM_011514768.1:c.	N/A	Intron Variant
CPNE5 transcript variant X2	XM_011514769.1:c.	N/A	Intron Variant
CPNE5 transcript variant X3	XM_011514770.1:c.	N/A	Intron Variant
CPNE5 transcript variant X4	XM_011514771.2:c.	N/A	Intron Variant
CPNE5 transcript variant X6	XM_011514772.1:c.	N/A	Intron Variant
CPNE5 transcript variant X7	XM_011514773.2:c.	N/A	Intron Variant
CPNE5 transcript variant X8	XM_017011139.1:c.	N/A	Intron Variant
CPNE5 transcript variant X11	XM_011514775.2:c.	N/A	Genic Upstream Transcript Variant
CPNE5 transcript variant X10	XR_001743541.1:n.	N/A	Intron Variant
CPNE5 transcript variant X12	XR_001743542.1:n.	N/A	Intron Variant
CPNE5 transcript variant X9	XR_926291.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.730	G=0.270
1000Genomes	American	Sub	694	C=0.950	G=0.050
1000Genomes	East Asian	Sub	1008	C=0.816	G=0.184
1000Genomes	Europe	Sub	1006	C=0.936	G=0.064
1000Genomes	Global	Study-wide	5008	C=0.866	G=0.134
1000Genomes	South Asian	Sub	978	C=0.970	G=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.956	G=0.044
The Genome Aggregation Database	African	Sub	8718	C=0.749	G=0.251
The Genome Aggregation Database	American	Sub	838	C=0.950	G=0.050
The Genome Aggregation Database	East Asian	Sub	1620	C=0.836	G=0.164
The Genome Aggregation Database	Europe	Sub	18502	C=0.944	G=0.055
The Genome Aggregation Database	Global	Study-wide	29980	C=0.881	G=0.118
The Genome Aggregation Database	Other	Sub	302	C=0.950	G=0.050
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.960	G=0.040

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
rs7769970	0.000149	alcohol dependence	21314694

eQTL of rs7769970 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 rs7769970 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.