rs4867084

Organism: Homo sapiens

Alleles: G>A / G>C / G>T

Gene : Feature

PDZD2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0380 (11392/29908,GnomAD)
A=0361 (10537/29118,TOPMED)
A=0344 (1725/5008,1000G)
A=0480 (1849/3854,ALSPAC)
A=0490 (1818/3708,TWINSUK)

Position: chr5:31818841 (GRCh38.p7) (5p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 18 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.31818841G>A
GRCh38.p7 chr 5	NC_000005.10:g.31818841G>C
GRCh38.p7 chr 5	NC_000005.10:g.31818841G>T
GRCh37.p13 chr 5	NC_000005.9:g.31818948G>A
GRCh37.p13 chr 5	NC_000005.9:g.31818948G>C
GRCh37.p13 chr 5	NC_000005.9:g.31818948G>T
PDZD2 RefSeqGene	NG_033962.2:g.184432G>A
PDZD2 RefSeqGene	NG_033962.2:g.184432G>C
PDZD2 RefSeqGene	NG_033962.2:g.184432G>T

Gene: PDZD2, PDZ domain containing 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PDZD2 transcript	NM_178140.3:c.	N/A	Intron Variant
PDZD2 transcript variant X2	XM_005248269.4:c.	N/A	Intron Variant
PDZD2 transcript variant X1	XM_011513992.2:c.	N/A	Intron Variant
PDZD2 transcript variant X3	XM_011513993.2:c.	N/A	Intron Variant
PDZD2 transcript variant X4	XM_011513994.2:c.	N/A	Intron Variant
PDZD2 transcript variant X5	XM_011513995.2:c.	N/A	Intron Variant
PDZD2 transcript variant X6	XM_011513996.2:c.	N/A	Intron Variant
PDZD2 transcript variant X10	XM_017009246.1:c.	N/A	Intron Variant
PDZD2 transcript variant X8	XM_005248271.1:c.	N/A	Genic Upstream Transcript Variant
PDZD2 transcript variant X7	XM_005248272.3:c.	N/A	Genic Upstream Transcript Variant
PDZD2 transcript variant X11	XM_006714460.2:c.	N/A	Genic Upstream Transcript Variant
PDZD2 transcript variant X9	XM_017009245.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.784	A=0.216
1000Genomes	American	Sub	694	G=0.520	A=0.480
1000Genomes	East Asian	Sub	1008	G=0.725	A=0.275
1000Genomes	Europe	Sub	1006	G=0.540	A=0.460
1000Genomes	Global	Study-wide	5008	G=0.656	A=0.344
1000Genomes	South Asian	Sub	978	G=0.620	A=0.380
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.520	A=0.480
The Genome Aggregation Database	African	Sub	8702	G=0.752	A=0.248
The Genome Aggregation Database	American	Sub	834	G=0.500	A=0.500
The Genome Aggregation Database	East Asian	Sub	1614	G=0.729	A=0.271
The Genome Aggregation Database	Europe	Sub	18458	G=0.552	A=0.447
The Genome Aggregation Database	Global	Study-wide	29908	G=0.619	A=0.380
The Genome Aggregation Database	Other	Sub	300	G=0.640	A=0.360
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.638	A=0.361
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.510	A=0.490

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
21072201	Genome-wide and follow-up studies identify CEP68 gene variants associated with risk of aspirin-intolerant asthma.	Kim JH	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs4867084	0.000651	alcohol dependence	21314694

eQTL of rs4867084 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 rs4867084 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.

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	101119139	101119471	E067	25009
chr5	101119595	101119645	E067	25465
chr5	101119139	101119471	E068	25009
chr5	101119595	101119645	E068	25465
chr5	101119139	101119471	E069	25009
chr5	101119595	101119645	E069	25465
chr5	101119139	101119471	E070	25009
chr5	101119595	101119645	E070	25465
chr5	101119139	101119471	E071	25009
chr5	101119595	101119645	E071	25465
chr5	101119139	101119471	E072	25009
chr5	101119595	101119645	E072	25465
chr5	101119139	101119471	E073	25009
chr5	101119595	101119645	E073	25465
chr5	101119139	101119471	E074	25009
chr5	101119595	101119645	E074	25465
chr5	101119139	101119471	E082	25009
chr5	101119595	101119645	E082	25465