SNP Detail Info-rs2824642

Organism: Homo sapiens

Alleles: C>G / C>T

Gene : Feature

CHODL : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0382 (11412/29872,GnomAD)
G=0396 (11554/29118,TOPMED)
G=0489 (2451/5008,1000G)
G=0258 (995/3854,ALSPAC)
G=0269 (999/3708,TWINSUK)

Position: chr21:18131787 (GRCh38.p7) (21q21.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 14 Enhancers around

Promoter: 4 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
CHODL transcript variant 3	NM_001204175.1:c.	N/A	Intron Variant
CHODL transcript variant 4	NM_001204176.1:c.	N/A	Intron Variant
CHODL transcript variant 5	NM_001204177.1:c.	N/A	Intron Variant
CHODL transcript variant 6	NM_001204178.1:c.	N/A	Intron Variant
CHODL transcript variant 2	NM_001204174.1:c.	N/A	Genic Upstream Transcript Variant
CHODL transcript variant 1	NM_024944.2:c.	N/A	Genic Upstream Transcript Variant
CHODL transcript variant X3	XM_011529457.2:c.	N/A	Intron Variant
CHODL transcript variant X2	XM_011529453.2:c.	N/A	Genic Upstream Transcript Variant
CHODL transcript variant X1	XM_017028273.1:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.486	G=0.514
1000Genomes	American	Sub	694	C=0.540	G=0.460
1000Genomes	East Asian	Sub	1008	C=0.263	G=0.737
1000Genomes	Europe	Sub	1006	C=0.719	G=0.281
1000Genomes	Global	Study-wide	5008	C=0.511	G=0.489
1000Genomes	South Asian	Sub	978	C=0.560	G=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.742	G=0.258
The Genome Aggregation Database	African	Sub	8692	C=0.496	G=0.504
The Genome Aggregation Database	American	Sub	834	C=0.510	G=0.490
The Genome Aggregation Database	East Asian	Sub	1616	C=0.263	G=0.737
The Genome Aggregation Database	Europe	Sub	18428	C=0.711	G=0.289
The Genome Aggregation Database	Global	Study-wide	29872	C=0.618	G=0.382
The Genome Aggregation Database	Other	Sub	302	C=0.630	G=0.370
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.603	G=0.396
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.731	G=0.269

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

SNP ID	p-value	Traits	Study
rs2824642	0.000171	nicotine smoking	19268276

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr21	36352535	36352620	E068	-24601
chr21	36352661	36352752	E068	-24469
chr21	36352767	36352835	E068	-24386
chr21	36352891	36353077	E068	-24144
chr21	36425623	36426088	E071	48402
chr21	36426132	36426204	E071	48911
chr21	36426268	36426320	E071	49047
chr21	36425623	36426088	E074	48402
chr21	36426132	36426204	E074	48911
chr21	36426268	36426320	E074	49047
chr21	36426592	36426642	E074	49371
chr21	36341752	36342065	E081	-35156
chr21	36342146	36342524	E081	-34697
chr21	36342534	36342648	E081	-34573

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr21	36419156	36422031	E068	41935
chr21	36419156	36422031	E069	41935
chr21	36419156	36422031	E071	41935
chr21	36419156	36422031	E074	41935

rs2824642