rs1935468

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

PCDH15 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0298 (8919/29900,GnomAD)
T==0259 (7548/29118,TOPMED)
T==0395 (1979/5008,1000G)
T==0289 (1112/3854,ALSPAC)
T==0301 (1115/3708,TWINSUK)

Position: chr10:54323965 (GRCh38.p7) (10q21.1)

Phenotype: ND

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.54323965T>C
GRCh37.p13 chr 10	NC_000010.10:g.56083725T>C
PCDH15 RefSeqGene	NG_009191.2:g.482327A>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	Intron Variant
PCDH15 transcript variant B	NM_001142764.1:c.	N/A	Intron Variant
PCDH15 transcript variant D	NM_001142765.1:c.	N/A	Intron Variant
PCDH15 transcript variant E	NM_001142766.1:c.	N/A	Intron Variant
PCDH15 transcript variant F	NM_001142767.1:c.	N/A	Intron Variant
PCDH15 transcript variant G	NM_001142768.1:c.	N/A	Intron Variant
PCDH15 transcript variant I	NM_001142769.1:c.	N/A	Intron Variant
PCDH15 transcript variant J	NM_001142770.1:c.	N/A	Intron Variant
PCDH15 transcript variant K	NM_001142771.1:c.	N/A	Intron Variant
PCDH15 transcript variant L	NM_001142772.1:c.	N/A	Intron Variant
PCDH15 transcript variant H	NM_001142773.1:c.	N/A	Intron Variant
PCDH15 transcript variant C	NM_033056.3:c.	N/A	Intron Variant
PCDH15 transcript variant X3	XM_017016571.1:c.	N/A	Intron Variant
PCDH15 transcript variant X4	XM_017016572.1:c.	N/A	Intron Variant
PCDH15 transcript variant X5	XM_017016573.1:c.	N/A	Intron Variant
PCDH15 transcript variant X1	XR_001747192.1:n.	N/A	Intron Variant
PCDH15 transcript variant X2	XR_001747193.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.235	C=0.765
1000Genomes	American	Sub	694	T=0.340	C=0.660
1000Genomes	East Asian	Sub	1008	T=0.773	C=0.227
1000Genomes	Europe	Sub	1006	T=0.253	C=0.747
1000Genomes	Global	Study-wide	5008	T=0.395	C=0.605
1000Genomes	South Asian	Sub	978	T=0.410	C=0.590
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.289	C=0.711
The Genome Aggregation Database	African	Sub	8708	T=0.253	C=0.747
The Genome Aggregation Database	American	Sub	838	T=0.380	C=0.620
The Genome Aggregation Database	East Asian	Sub	1602	T=0.759	C=0.241
The Genome Aggregation Database	Europe	Sub	18450	T=0.276	C=0.723
The Genome Aggregation Database	Global	Study-wide	29900	T=0.298	C=0.701
The Genome Aggregation Database	Other	Sub	302	T=0.270	C=0.730
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.259	C=0.740
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.301	C=0.699

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs1935468	1.58E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs1935468 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 rs1935468 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.