rs10825471

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PCDH15 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0367 (10956/29844,GnomAD)
G=0371 (10821/29118,TOPMED)
G=0316 (1581/5008,1000G)
G=0396 (1526/3854,ALSPAC)
G=0409 (1518/3708,TWINSUK)

Position: chr10:55140878 (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.55140878A>G
GRCh37.p13 chr 10	NC_000010.10:g.56900638A>G

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	A=0.700	G=0.300
1000Genomes	American	Sub	694	A=0.530	G=0.470
1000Genomes	East Asian	Sub	1008	A=0.844	G=0.156
1000Genomes	Europe	Sub	1006	A=0.602	G=0.398
1000Genomes	Global	Study-wide	5008	A=0.684	G=0.316
1000Genomes	South Asian	Sub	978	A=0.690	G=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.604	G=0.396
The Genome Aggregation Database	African	Sub	8698	A=0.672	G=0.328
The Genome Aggregation Database	American	Sub	836	A=0.510	G=0.490
The Genome Aggregation Database	East Asian	Sub	1604	A=0.853	G=0.147
The Genome Aggregation Database	Europe	Sub	18404	A=0.601	G=0.398
The Genome Aggregation Database	Global	Study-wide	29844	A=0.632	G=0.367
The Genome Aggregation Database	Other	Sub	302	A=0.590	G=0.410
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.628	G=0.371
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.591	G=0.409

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
rs10825471	0.000836	alcohol dependence	20201924

eQTL of rs10825471 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 rs10825471 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.