rs7206133

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

CDH13 : Intron Variant
LOC105371366 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0176 (5274/29924,GnomAD)
G=0193 (5644/29118,TOPMED)
G=0155 (777/5008,1000G)
G=0181 (698/3854,ALSPAC)
G=0172 (638/3708,TWINSUK)

Position: chr16:83728501 (GRCh38.p7) (16q23.3)

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 16	NC_000016.10:g.83728501A>G
GRCh38.p7 chr 16	NC_000016.10:g.83728501A>T
GRCh37.p13 chr 16	NC_000016.9:g.83762106A>G
GRCh37.p13 chr 16	NC_000016.9:g.83762106A>T

Gene: CDH13, cadherin 13(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CDH13 transcript variant 2	NM_001220488.1:c.	N/A	Intron Variant
CDH13 transcript variant 3	NM_001220489.1:c.	N/A	Intron Variant
CDH13 transcript variant 4	NM_001220490.1:c.	N/A	Intron Variant
CDH13 transcript variant 1	NM_001257.4:c.	N/A	Intron Variant
CDH13 transcript variant 5	NM_001220491.1:c.	N/A	Genic Downstream Transcript Variant
CDH13 transcript variant 6	NM_001220492.1:c.	N/A	Genic Downstream Transcript Variant
CDH13 transcript variant X1	XM_011522804.2:c.	N/A	Intron Variant
CDH13 transcript variant X2	XM_017022848.1:c.	N/A	Genic Downstream Transcript Variant
CDH13 transcript variant X3	XM_017022849.1:c.	N/A	Genic Downstream Transcript Variant

Gene: LOC105371366, uncharacterized LOC105371366(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371366 transcript variant X1	XR_001752382.1:n.	N/A	Intron Variant
LOC105371366 transcript variant X3	XR_933801.2:n.	N/A	Intron Variant
LOC105371366 transcript variant X4	XR_001752383.1:n.	N/A	Genic Upstream Transcript Variant
LOC105371366 transcript variant X5	XR_001752384.1:n.	N/A	Genic Upstream Transcript Variant
LOC105371366 transcript variant X6	XR_001752385.1:n.	N/A	Genic Upstream Transcript Variant
LOC105371366 transcript variant X2	XR_933802.2:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.793	G=0.207
1000Genomes	American	Sub	694	A=0.850	G=0.150
1000Genomes	East Asian	Sub	1008	A=0.937	G=0.063
1000Genomes	Europe	Sub	1006	A=0.807	G=0.193
1000Genomes	Global	Study-wide	5008	A=0.845	G=0.155
1000Genomes	South Asian	Sub	978	A=0.860	G=0.140
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.819	G=0.181
The Genome Aggregation Database	African	Sub	8696	A=0.801	T=0.000
The Genome Aggregation Database	American	Sub	838	A=0.890	T=0.00,
The Genome Aggregation Database	East Asian	Sub	1616	A=0.944	T=0.001
The Genome Aggregation Database	Europe	Sub	18474	A=0.821	T=0.000
The Genome Aggregation Database	Global	Study-wide	29924	A=0.823	T=0.000
The Genome Aggregation Database	Other	Sub	300	A=0.800	T=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.806	G=0.193
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.828	G=0.172

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs7206133	0.000694	nicotine smoking	19268276

eQTL of rs7206133 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 rs7206133 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.