rs2247977

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PCDH15 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0055 (1662/29950,GnomAD)
G==0061 (1799/29118,TOPMED)
G==0072 (359/5008,1000G)
G==0052 (200/3854,ALSPAC)
G==0050 (186/3708,TWINSUK)

Position: chr10:55213052 (GRCh38.p7) (10q21.1)

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 10	NC_000010.11:g.55213052G>A
GRCh37.p13 chr 10	NC_000010.10:g.56972812G>A

Gene: PCDH15, protocadherin-related 15(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PCDH15 transcript variant A	NM_001142763.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant B	NM_001142764.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant D	NM_001142765.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant E	NM_001142766.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant F	NM_001142767.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant G	NM_001142768.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant I	NM_001142769.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant J	NM_001142770.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant K	NM_001142771.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant L	NM_001142772.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant H	NM_001142773.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant C	NM_033056.3:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant X5	XM_017016573.1:c.	N/A	Intron Variant
PCDH15 transcript variant X3	XM_017016571.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant X4	XM_017016572.1:c.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant X1	XR_001747192.1:n.	N/A	Genic Upstream Transcript Variant
PCDH15 transcript variant X2	XR_001747193.1:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.067	A=0.933
1000Genomes	American	Sub	694	G=0.040	A=0.960
1000Genomes	East Asian	Sub	1008	G=0.110	A=0.890
1000Genomes	Europe	Sub	1006	G=0.059	A=0.941
1000Genomes	Global	Study-wide	5008	G=0.072	A=0.928
1000Genomes	South Asian	Sub	978	G=0.080	A=0.920
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.052	A=0.948
The Genome Aggregation Database	African	Sub	8706	G=0.069	A=0.931
The Genome Aggregation Database	American	Sub	838	G=0.050	A=0.950
The Genome Aggregation Database	East Asian	Sub	1614	G=0.082	A=0.918
The Genome Aggregation Database	Europe	Sub	18490	G=0.047	A=0.952
The Genome Aggregation Database	Global	Study-wide	29950	G=0.055	A=0.944
The Genome Aggregation Database	Other	Sub	302	G=0.070	A=0.930
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.061	A=0.938
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.050	A=0.950

PMID	Title	Author	Journal
21529783	A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.	Heath AC	Biol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs2247977	6.5E-05	alcoholism (heaviness of drinking)	21529783

eQTL of rs2247977 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 rs2247977 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.