rs2238796

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

ARVCF : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0020 (611/29930,GnomAD)
T=0025 (731/29116,TOPMED)
T=0036 (179/5008,1000G)

Position: chr22:20011550 (GRCh38.p7) (22q11.21)

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 22	NC_000022.11:g.20011550C>A
GRCh38.p7 chr 22	NC_000022.11:g.20011550C>T
GRCh37.p13 chr 22	NC_000022.10:g.19999073C>A
GRCh37.p13 chr 22	NC_000022.10:g.19999073C>T
ARVCF RefSeqGene	NG_023326.1:g.10237G>T
ARVCF RefSeqGene	NG_023326.1:g.10237G>A

Gene: ARVCF, armadillo repeat gene deleted in velocardiofacial syndrome(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARVCF transcript	NM_001670.2:c.	N/A	Intron Variant
ARVCF transcript variant X2	XM_005261242.2:c.	N/A	Intron Variant
ARVCF transcript variant X5	XM_005261243.3:c.	N/A	Intron Variant
ARVCF transcript variant X7	XM_005261244.3:c.	N/A	Intron Variant
ARVCF transcript variant X1	XM_006724243.2:c.	N/A	Intron Variant
ARVCF transcript variant X6	XM_006724245.2:c.	N/A	Intron Variant
ARVCF transcript variant X14	XM_006724249.3:c.	N/A	Intron Variant
ARVCF transcript variant X15	XM_006724250.3:c.	N/A	Intron Variant
ARVCF transcript variant X3	XM_011530179.2:c.	N/A	Intron Variant
ARVCF transcript variant X4	XM_011530180.1:c.	N/A	Intron Variant
ARVCF transcript variant X16	XM_011530181.1:c.	N/A	Intron Variant
ARVCF transcript variant X8	XM_006724246.3:c.	N/A	Genic Upstream Transcript Variant
ARVCF transcript variant X9	XM_006724247.3:c.	N/A	Genic Upstream Transcript Variant
ARVCF transcript variant X10	XM_006724248.3:c.	N/A	Genic Upstream Transcript Variant
ARVCF transcript variant X16	XM_011530182.2:c.	N/A	Genic Upstream Transcript Variant
ARVCF transcript variant X17	XM_011530183.2:c.	N/A	Genic Upstream Transcript Variant
ARVCF transcript variant X11	XR_937863.1:n.	N/A	Intron Variant
ARVCF transcript variant X13	XR_937864.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.967	T=0.033
1000Genomes	American	Sub	694	C=0.950	T=0.050
1000Genomes	East Asian	Sub	1008	C=0.913	T=0.087
1000Genomes	Europe	Sub	1006	C=0.991	T=0.009
1000Genomes	Global	Study-wide	5008	C=0.964	T=0.036
1000Genomes	South Asian	Sub	978	C=0.990	T=0.010
The Genome Aggregation Database	African	Sub	8706	C=0.969	T=0.031
The Genome Aggregation Database	American	Sub	838	C=0.960	T=0.040
The Genome Aggregation Database	East Asian	Sub	1622	C=0.924	T=0.076
The Genome Aggregation Database	Europe	Sub	18462	C=0.990	T=0.009
The Genome Aggregation Database	Global	Study-wide	29930	C=0.979	T=0.020
The Genome Aggregation Database	Other	Sub	302	C=1.000	T=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.974	T=0.025

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
rs2238796	0.000353	nicotine smoking	19268276

eQTL of rs2238796 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 rs2238796 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.