rs17739703

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CCDC178 : Intron Variant
LOC105372059 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0051 (1531/29946,GnomAD)
C=0038 (1114/29118,TOPMED)
C=0022 (112/5008,1000G)
C=0069 (264/3854,ALSPAC)
C=0066 (245/3708,TWINSUK)

Position: chr18:32943324 (GRCh38.p7) (18q12.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 6 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 18	NC_000018.10:g.32943324T>C
GRCh37.p13 chr 18	NC_000018.9:g.30523288T>C

Gene: CCDC178, coiled-coil domain containing 178(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CCDC178 transcript variant 1	NM_001105528.1:c.	N/A	Intron Variant
CCDC178 transcript variant 3	NM_001308126.1:c.	N/A	Intron Variant
CCDC178 transcript variant 2	NM_198995.2:c.	N/A	Intron Variant
CCDC178 transcript variant X4	XM_011525948.1:c.	N/A	Intron Variant
CCDC178 transcript variant X5	XM_011525951.1:c.	N/A	Intron Variant
CCDC178 transcript variant X1	XM_017025721.1:c.	N/A	Intron Variant
CCDC178 transcript variant X2	XM_017025722.1:c.	N/A	Intron Variant
CCDC178 transcript variant X3	XM_017025723.1:c.	N/A	Intron Variant
CCDC178 transcript variant X6	XM_017025724.1:c.	N/A	Intron Variant
CCDC178 transcript variant X7	XM_017025725.1:c.	N/A	Intron Variant
CCDC178 transcript variant X8	XM_011525954.2:c.	N/A	Genic Downstream Transcript Variant
CCDC178 transcript variant X9	XM_011525955.1:c.	N/A	Genic Downstream Transcript Variant

Gene: LOC105372059, uncharacterized LOC105372059(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372059 transcript variant X1	XR_001753402.1:n.	N/A	Intron Variant
LOC105372059 transcript variant X4	XR_935363.2:n.	N/A	Intron Variant
LOC105372059 transcript variant X2	XR_935365.2:n.	N/A	Intron Variant
LOC105372059 transcript variant X3	XR_935364.2:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.998	C=0.002
1000Genomes	American	Sub	694	T=0.980	C=0.020
1000Genomes	East Asian	Sub	1008	T=1.000	C=0.000
1000Genomes	Europe	Sub	1006	T=0.928	C=0.072
1000Genomes	Global	Study-wide	5008	T=0.978	C=0.022
1000Genomes	South Asian	Sub	978	T=0.980	C=0.020
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.931	C=0.069
The Genome Aggregation Database	African	Sub	8728	T=0.987	C=0.013
The Genome Aggregation Database	American	Sub	838	T=0.970	C=0.030
The Genome Aggregation Database	East Asian	Sub	1616	T=0.999	C=0.001
The Genome Aggregation Database	Europe	Sub	18462	T=0.925	C=0.074
The Genome Aggregation Database	Global	Study-wide	29946	T=0.948	C=0.051
The Genome Aggregation Database	Other	Sub	302	T=0.970	C=0.030
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.961	C=0.038
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.934	C=0.066

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
rs17739703	6.69E-05	nicotine smoking	19268276

eQTL of rs17739703 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 rs17739703 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 )
chr18	30485404	30486097	E081	-37191
chr18	30486668	30486776	E081	-36512
chr18	30495603	30495780	E081	-27508
chr18	30498686	30499264	E081	-24024
chr18	30537495	30537582	E081	14207
chr18	30537710	30537760	E081	14422