rs6807897

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LPP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0145 (4360/29964,GnomAD)
A=0169 (4926/29118,TOPMED)
A=0132 (660/5008,1000G)
A=0093 (360/3854,ALSPAC)
A=0097 (358/3708,TWINSUK)

Position: chr3:188515616 (GRCh38.p7) (3q28)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 100 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.188515616G>A
GRCh37.p13 chr 3	NC_000003.11:g.188233404G>A
LPP RefSeqGene	NG_016932.2:g.366742G>A

Gene: LPP, LIM domain containing preferred translocation partner in lipoma(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LPP transcript variant 2	NM_001167671.2:c.	N/A	Intron Variant
LPP transcript variant 3	NM_001167672.2:c.	N/A	Intron Variant
LPP transcript variant 1	NM_005578.4:c.	N/A	Intron Variant
LPP transcript variant X4	XM_005247446.4:c.	N/A	Intron Variant
LPP transcript variant X13	XM_005247450.4:c.	N/A	Intron Variant
LPP transcript variant X8	XM_005247451.4:c.	N/A	Intron Variant
LPP transcript variant X13	XM_005247453.2:c.	N/A	Intron Variant
LPP transcript variant X4	XM_011512820.2:c.	N/A	Intron Variant
LPP transcript variant X1	XM_011512823.2:c.	N/A	Intron Variant
LPP transcript variant X11	XM_011512827.2:c.	N/A	Intron Variant
LPP transcript variant X14	XM_011512828.2:c.	N/A	Intron Variant
LPP transcript variant X15	XM_011512831.2:c.	N/A	Intron Variant
LPP transcript variant X3	XM_011512833.2:c.	N/A	Intron Variant
LPP transcript variant X2	XM_011512834.2:c.	N/A	Intron Variant
LPP transcript variant X6	XM_017006377.1:c.	N/A	Intron Variant
LPP transcript variant X7	XM_017006378.1:c.	N/A	Intron Variant
LPP transcript variant X9	XM_017006379.1:c.	N/A	Intron Variant
LPP transcript variant X11	XM_017006380.1:c.	N/A	Intron Variant
LPP transcript variant X18	XM_017006381.1:c.	N/A	Intron Variant
LPP transcript variant X19	XM_017006382.1:c.	N/A	Intron Variant
LPP transcript variant X19	XM_011512836.2:c.	N/A	Genic Upstream Transcript Variant
LPP transcript variant X17	XR_001740144.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.700	A=0.300
1000Genomes	American	Sub	694	G=0.900	A=0.100
1000Genomes	East Asian	Sub	1008	G=0.927	A=0.073
1000Genomes	Europe	Sub	1006	G=0.908	A=0.092
1000Genomes	Global	Study-wide	5008	G=0.868	A=0.132
1000Genomes	South Asian	Sub	978	G=0.970	A=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.907	A=0.093
The Genome Aggregation Database	African	Sub	8706	G=0.728	A=0.272
The Genome Aggregation Database	American	Sub	838	G=0.920	A=0.080
The Genome Aggregation Database	East Asian	Sub	1616	G=0.911	A=0.089
The Genome Aggregation Database	Europe	Sub	18502	G=0.905	A=0.094
The Genome Aggregation Database	Global	Study-wide	29964	G=0.854	A=0.145
The Genome Aggregation Database	Other	Sub	302	G=0.880	A=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.830	A=0.169
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.903	A=0.097

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
rs6807897	0.000715	nicotine smoking	19268276

eQTL of rs6807897 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 rs6807897 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 )
chr3	188186123	188186228	E067	-47176
chr3	188186261	188186356	E067	-47048
chr3	188186443	188186879	E067	-46525
chr3	188189636	188189876	E067	-43528
chr3	188190066	188190223	E067	-43181
chr3	188190266	188190406	E067	-42998
chr3	188190430	188190599	E067	-42805
chr3	188209095	188209515	E067	-23889
chr3	188209523	188209656	E067	-23748
chr3	188209694	188209761	E067	-23643
chr3	188209762	188209937	E067	-23467
chr3	188251528	188251630	E067	18124
chr3	188251987	188252233	E067	18583
chr3	188252385	188252702	E067	18981
chr3	188185941	188185991	E068	-47413
chr3	188186123	188186228	E068	-47176
chr3	188186261	188186356	E068	-47048
chr3	188186443	188186879	E068	-46525
chr3	188186886	188187561	E068	-45843
chr3	188189636	188189876	E068	-43528
chr3	188190066	188190223	E068	-43181
chr3	188190266	188190406	E068	-42998
chr3	188190430	188190599	E068	-42805
chr3	188194647	188195127	E068	-38277
chr3	188197884	188198101	E068	-35303
chr3	188198584	188198662	E068	-34742
chr3	188209095	188209515	E068	-23889
chr3	188209523	188209656	E068	-23748
chr3	188209694	188209761	E068	-23643
chr3	188209762	188209937	E068	-23467
chr3	188243855	188244194	E068	10451
chr3	188185941	188185991	E069	-47413
chr3	188186123	188186228	E069	-47176
chr3	188186261	188186356	E069	-47048
chr3	188186443	188186879	E069	-46525
chr3	188186886	188187561	E069	-45843
chr3	188194647	188195127	E069	-38277
chr3	188198584	188198662	E069	-34742
chr3	188251987	188252233	E069	18583
chr3	188252385	188252702	E069	18981
chr3	188189636	188189876	E070	-43528
chr3	188190066	188190223	E070	-43181
chr3	188190266	188190406	E070	-42998
chr3	188225968	188226022	E070	-7382
chr3	188226223	188226578	E070	-6826
chr3	188186123	188186228	E071	-47176
chr3	188186261	188186356	E071	-47048
chr3	188186443	188186879	E071	-46525
chr3	188186886	188187561	E071	-45843
chr3	188189461	188189511	E071	-43893
chr3	188189636	188189876	E071	-43528
chr3	188190066	188190223	E071	-43181
chr3	188194647	188195127	E071	-38277
chr3	188225968	188226022	E071	-7382
chr3	188251528	188251630	E071	18124
chr3	188251987	188252233	E071	18583
chr3	188252385	188252702	E071	18981
chr3	188276882	188277120	E071	43478
chr3	188185941	188185991	E072	-47413
chr3	188186123	188186228	E072	-47176
chr3	188186261	188186356	E072	-47048
chr3	188186886	188187561	E072	-45843
chr3	188189636	188189876	E072	-43528
chr3	188190066	188190223	E072	-43181
chr3	188190266	188190406	E072	-42998
chr3	188190430	188190599	E072	-42805
chr3	188251987	188252233	E072	18583
chr3	188252385	188252702	E072	18981
chr3	188186443	188186879	E073	-46525
chr3	188190066	188190223	E073	-43181
chr3	188190266	188190406	E073	-42998
chr3	188190430	188190599	E073	-42805
chr3	188194647	188195127	E073	-38277
chr3	188197884	188198101	E073	-35303
chr3	188251528	188251630	E073	18124
chr3	188251987	188252233	E073	18583
chr3	188252385	188252702	E073	18981
chr3	188185941	188185991	E074	-47413
chr3	188186123	188186228	E074	-47176
chr3	188186261	188186356	E074	-47048
chr3	188186443	188186879	E074	-46525
chr3	188186886	188187561	E074	-45843
chr3	188188307	188188505	E074	-44899
chr3	188194647	188195127	E074	-38277
chr3	188207815	188208147	E074	-25257
chr3	188209095	188209515	E074	-23889
chr3	188209523	188209656	E074	-23748
chr3	188209694	188209761	E074	-23643
chr3	188209762	188209937	E074	-23467
chr3	188231584	188231985	E074	-1419
chr3	188251987	188252233	E074	18583
chr3	188197884	188198101	E081	-35303
chr3	188198584	188198662	E081	-34742
chr3	188199382	188199470	E081	-33934
chr3	188225535	188225616	E081	-7788
chr3	188225968	188226022	E081	-7382
chr3	188226223	188226578	E081	-6826
chr3	188228054	188228173	E081	-5231
chr3	188197884	188198101	E082	-35303
chr3	188228194	188228578	E082	-4826