rs10785246

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PDZRN4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0104 (3133/29902,GnomAD)
C==0119 (3468/29118,TOPMED)
C==0149 (746/5008,1000G)
C==0086 (332/3854,ALSPAC)
C==0073 (271/3708,TWINSUK)

Position: chr12:41353626 (GRCh38.p7) (12q12)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 54 Enhancers around

Promoter: 16 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.41353626C>T
GRCh37.p13 chr 12	NC_000012.11:g.41747428C>T

Gene: PDZRN4, PDZ domain containing ring finger 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PDZRN4 transcript variant 1	NM_001164595.1:c.	N/A	Intron Variant
PDZRN4 transcript variant 2	NM_013377.3:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.225	T=0.775
1000Genomes	American	Sub	694	C=0.060	T=0.940
1000Genomes	East Asian	Sub	1008	C=0.163	T=0.837
1000Genomes	Europe	Sub	1006	C=0.077	T=0.923
1000Genomes	Global	Study-wide	5008	C=0.149	T=0.851
1000Genomes	South Asian	Sub	978	C=0.170	T=0.830
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.086	T=0.914
The Genome Aggregation Database	African	Sub	8702	C=0.183	T=0.817
The Genome Aggregation Database	American	Sub	838	C=0.060	T=0.940
The Genome Aggregation Database	East Asian	Sub	1580	C=0.177	T=0.823
The Genome Aggregation Database	Europe	Sub	18480	C=0.063	T=0.937
The Genome Aggregation Database	Global	Study-wide	29902	C=0.104	T=0.895
The Genome Aggregation Database	Other	Sub	302	C=0.150	T=0.850
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.119	T=0.880
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.073	T=0.927

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
rs10785246	4.67E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs10785246 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 rs10785246 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.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr12	41698526	41698645	E067	-48783
chr12	41698729	41698779	E067	-48649
chr12	41728216	41728489	E067	-18939
chr12	41756396	41756589	E067	8968
chr12	41697633	41697685	E068	-49743
chr12	41697723	41697779	E068	-49649
chr12	41728216	41728489	E068	-18939
chr12	41697633	41697685	E069	-49743
chr12	41697723	41697779	E069	-49649
chr12	41698526	41698645	E069	-48783
chr12	41728216	41728489	E069	-18939
chr12	41756396	41756589	E069	8968
chr12	41726595	41726645	E070	-20783
chr12	41727759	41727881	E070	-19547
chr12	41727892	41728030	E070	-19398
chr12	41728216	41728489	E070	-18939
chr12	41730073	41730238	E070	-17190
chr12	41756396	41756589	E070	8968
chr12	41756929	41757010	E070	9501
chr12	41757301	41757351	E070	9873
chr12	41757423	41757551	E070	9995
chr12	41757619	41757767	E070	10191
chr12	41758363	41758423	E070	10935
chr12	41759493	41759895	E070	12065
chr12	41790987	41791405	E070	43559
chr12	41791485	41791539	E070	44057
chr12	41791964	41792067	E070	44536
chr12	41792129	41792184	E070	44701
chr12	41793827	41793942	E070	46399
chr12	41697633	41697685	E071	-49743
chr12	41697723	41697779	E071	-49649
chr12	41728216	41728489	E071	-18939
chr12	41756396	41756589	E071	8968
chr12	41756929	41757010	E071	9501
chr12	41759493	41759895	E071	12065
chr12	41793827	41793942	E071	46399
chr12	41756396	41756589	E072	8968
chr12	41697633	41697685	E074	-49743
chr12	41697723	41697779	E074	-49649
chr12	41698526	41698645	E074	-48783
chr12	41698729	41698779	E074	-48649
chr12	41720913	41721035	E074	-26393
chr12	41721041	41721157	E074	-26271
chr12	41721225	41721510	E074	-25918
chr12	41727759	41727881	E074	-19547
chr12	41727892	41728030	E074	-19398
chr12	41728216	41728489	E074	-18939
chr12	41756396	41756589	E074	8968
chr12	41793827	41793942	E074	46399
chr12	41706764	41706814	E081	-40614
chr12	41754883	41754946	E081	7455
chr12	41727759	41727881	E082	-19547
chr12	41727892	41728030	E082	-19398
chr12	41728216	41728489	E082	-18939

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	41738760	41739221	E067	-8207
chr12	41739229	41739470	E067	-7958
chr12	41738760	41739221	E068	-8207
chr12	41739229	41739470	E068	-7958
chr12	41738760	41739221	E069	-8207
chr12	41739229	41739470	E069	-7958
chr12	41738760	41739221	E070	-8207
chr12	41739229	41739470	E070	-7958
chr12	41738760	41739221	E071	-8207
chr12	41739229	41739470	E071	-7958
chr12	41738760	41739221	E072	-8207
chr12	41739229	41739470	E072	-7958
chr12	41738760	41739221	E073	-8207
chr12	41739229	41739470	E073	-7958
chr12	41738760	41739221	E074	-8207
chr12	41739229	41739470	E074	-7958