rs17839323

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CDH12 : Synonymous Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0072 (8736/119804,ExAC)
G=0053 (1612/29956,GnomAD)
G=0050 (1455/29118,TOPMED)
A==0048 (635/13006,GO-ESP)
G=0061 (305/5008,1000G)
G=0053 (204/3854,ALSPAC)
G=0054 (199/3708,TWINSUK)

Position: chr5:21842327 (GRCh38.p7) (5p14.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 2 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.21842327A>G
GRCh37.p13 chr 5	NC_000005.9:g.21842436A>G

Gene: CDH12, cadherin 12(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CDH12 transcript variant 1	NM_004061.4:c.648T>C	G [GGT]> G [GGC]	Coding Sequence Variant
cadherin-12 isoform 1 preproprotein	NP_004052.2:p.Gly...NP_004052.2:p.Gly216=	G [Gly]> G [Gly]	Synonymous Variant
CDH12 transcript variant 2	NM_001317227.1:c....NM_001317227.1:c.648T>C	G [GGT]> G [GGC]	Coding Sequence Variant
cadherin-12 isoform 1 preproprotein	NP_001304156.1:p....NP_001304156.1:p.Gly216=	G [Gly]> G [Gly]	Synonymous Variant
CDH12 transcript variant 3	NM_001317228.1:c....NM_001317228.1:c.528T>C	G [GGT]> G [GGC]	Coding Sequence Variant
cadherin-12 isoform 2 precursor	NP_001304157.1:p....NP_001304157.1:p.Gly176=	G [Gly]> G [Gly]	Synonymous Variant
CDH12 transcript variant X1	XM_017008920.1:c....XM_017008920.1:c.648T>C	G [GGT]> G [GGC]	Coding Sequence Variant
cadherin-12 isoform X1	XP_016864409.1:p....XP_016864409.1:p.Gly216=	G [Gly]> G [Gly]	Synonymous Variant
CDH12 transcript variant X2	XM_011513927.2:c....XM_011513927.2:c.648T>C	G [GGT]> G [GGC]	Coding Sequence Variant
cadherin-12 isoform X1	XP_011512229.1:p....XP_011512229.1:p.Gly216=	G [Gly]> G [Gly]	Synonymous Variant
CDH12 transcript variant X3	XM_017008921.1:c....XM_017008921.1:c.648T>C	G [GGT]> G [GGC]	Coding Sequence Variant
cadherin-12 isoform X1	XP_016864410.1:p....XP_016864410.1:p.Gly216=	G [Gly]> G [Gly]	Synonymous Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.957	G=0.043
1000Genomes	American	Sub	694	A=0.890	G=0.110
1000Genomes	East Asian	Sub	1008	A=0.982	G=0.018
1000Genomes	Europe	Sub	1006	A=0.951	G=0.049
1000Genomes	Global	Study-wide	5008	A=0.939	G=0.061
1000Genomes	South Asian	Sub	978	A=0.890	G=0.110
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.947	G=0.053
The Exome Aggregation Consortium	American	Sub	21838	A=0.897	G=0.102
The Exome Aggregation Consortium	Asian	Sub	24364	A=0.915	G=0.084
The Exome Aggregation Consortium	Europe	Sub	72706	A=0.939	G=0.060
The Exome Aggregation Consortium	Global	Study-wide	119804	A=0.927	G=0.072
The Exome Aggregation Consortium	Other	Sub	896	A=0.940	G=0.060
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.950	G=0.050
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.946	G=0.054

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

P-Value

SNP ID	p-value	Traits	Study
rs17839323	0.000487	nicotine dependence	17158188

eQTL of rs17839323 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 rs17839323 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	21818241	21818338	E068	-24098
chr5	21818438	21818567	E068	-23869