SNP Detail Info-rs6463462

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

UPP1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0417 (12479/29868,GnomAD)
G==0402 (11716/29118,TOPMED)
G==0407 (2037/5008,1000G)
G==0427 (1646/3854,ALSPAC)
G==0419 (1554/3708,TWINSUK)

Position: chr7:48102597 (GRCh38.p7) (7p12.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 8 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.48102597G>T
GRCh37.p13 chr 7	NC_000007.13:g.48142194G>T

Molecule type	Change	Amino acid[Codon]	SO Term
UPP1 transcript variant 3	NM_001287426.1:c.	N/A	Intron Variant
UPP1 transcript variant 4	NM_001287428.1:c.	N/A	Intron Variant
UPP1 transcript variant 5	NM_001287429.1:c.	N/A	Intron Variant
UPP1 transcript variant 6	NM_001287430.1:c.	N/A	Intron Variant
UPP1 transcript variant 1	NM_003364.3:c.	N/A	Intron Variant
UPP1 transcript variant 7	NR_109837.1:n.	N/A	Intron Variant
UPP1 transcript variant X3	XM_005249838.4:c.	N/A	Intron Variant
UPP1 transcript variant X2	XM_011515512.2:c.	N/A	Intron Variant
UPP1 transcript variant X4	XM_011515513.2:c.	N/A	Intron Variant
UPP1 transcript variant X5	XM_011515514.2:c.	N/A	Intron Variant
UPP1 transcript variant X6	XM_011515515.2:c.	N/A	Intron Variant
UPP1 transcript variant X7	XR_001744869.1:n.	N/A	Intron Variant
UPP1 transcript variant X8	XR_001744870.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.393	T=0.607
1000Genomes	American	Sub	694	G=0.440	T=0.560
1000Genomes	East Asian	Sub	1008	G=0.477	T=0.523
1000Genomes	Europe	Sub	1006	G=0.398	T=0.602
1000Genomes	Global	Study-wide	5008	G=0.407	T=0.593
1000Genomes	South Asian	Sub	978	G=0.340	T=0.660
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.427	T=0.573
The Genome Aggregation Database	African	Sub	8688	G=0.392	T=0.608
The Genome Aggregation Database	American	Sub	836	G=0.440	T=0.560
The Genome Aggregation Database	East Asian	Sub	1614	G=0.467	T=0.533
The Genome Aggregation Database	Europe	Sub	18428	G=0.425	T=0.574
The Genome Aggregation Database	Global	Study-wide	29868	G=0.417	T=0.582
The Genome Aggregation Database	Other	Sub	302	G=0.350	T=0.650
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.402	T=0.597
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.419	T=0.581

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
rs6463462	7.96E-05	nicotine smoking	19268276

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr7:48142194	UPP1	ENSG00000183696.9	G>T	2.1763e-10	13969	Cerebellum

Probe ID	Position	Gene	beta	p-value
cg02006203	chr7:48128151	UPP1	-0.0168606934002853	4.7247e-11

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr7	48146636	48146686	E072	4442
chr7	48146348	48146567	E073	4154
chr7	48146636	48146686	E073	4442
chr7	48146850	48146945	E073	4656
chr7	48135062	48135102	E081	-7092
chr7	48135107	48135362	E081	-6832
chr7	48134356	48134999	E082	-7195

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	48127896	48130385	E067	-11809
chr7	48127896	48130385	E068	-11809
chr7	48127896	48130385	E069	-11809
chr7	48127896	48130385	E071	-11809
chr7	48127896	48130385	E072	-11809
chr7	48127896	48130385	E073	-11809
chr7	48127896	48130385	E074	-11809
chr7	48127896	48130385	E082	-11809

rs6463462