rs2054128

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LRRK1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0137 (4102/29944,GnomAD)
A=0134 (3921/29118,TOPMED)
A=0103 (515/5008,1000G)
A=0112 (432/3854,ALSPAC)
A=0117 (432/3708,TWINSUK)

Position: chr15:101001562 (GRCh38.p7) (15q26.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 31 Enhancers around

Promoter: 32 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.101001562G>A
GRCh37.p13 chr 15	NC_000015.9:g.101541767G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LRRK1 transcript	NM_024652.4:c.	N/A	Intron Variant
LRRK1 transcript variant X1	XM_011522012.2:c.	N/A	Intron Variant
LRRK1 transcript variant X2	XM_011522013.2:c.	N/A	Intron Variant
LRRK1 transcript variant X3	XM_011522014.2:c.	N/A	Intron Variant
LRRK1 transcript variant X4	XM_011522015.2:c.	N/A	Intron Variant
LRRK1 transcript variant X5	XM_011522016.2:c.	N/A	Intron Variant
LRRK1 transcript variant X11	XM_011522019.2:c.	N/A	Intron Variant
LRRK1 transcript variant X9	XM_005254979.3:c.	N/A	Genic Upstream Transcript Variant
LRRK1 transcript variant X8	XM_011522017.2:c.	N/A	Genic Upstream Transcript Variant
LRRK1 transcript variant X10	XM_011522018.2:c.	N/A	Genic Upstream Transcript Variant
LRRK1 transcript variant X6	XM_017022570.1:c.	N/A	Genic Upstream Transcript Variant
LRRK1 transcript variant X7	XR_931905.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.828	A=0.172
1000Genomes	American	Sub	694	G=0.940	A=0.060
1000Genomes	East Asian	Sub	1008	G=0.980	A=0.020
1000Genomes	Europe	Sub	1006	G=0.863	A=0.137
1000Genomes	Global	Study-wide	5008	G=0.897	A=0.103
1000Genomes	South Asian	Sub	978	G=0.910	A=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.888	A=0.112
The Genome Aggregation Database	African	Sub	8706	G=0.810	A=0.190
The Genome Aggregation Database	American	Sub	838	G=0.930	A=0.070
The Genome Aggregation Database	East Asian	Sub	1620	G=0.983	A=0.017
The Genome Aggregation Database	Europe	Sub	18478	G=0.874	A=0.126
The Genome Aggregation Database	Global	Study-wide	29944	G=0.863	A=0.137
The Genome Aggregation Database	Other	Sub	302	G=0.880	A=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.865	A=0.134
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.883	A=0.117

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
rs2054128	0.000936	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

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr15	101547090	101548240	E067	5323
chr15	101563568	101564795	E067	21801
chr15	101564915	101565077	E067	23148
chr15	101555430	101555954	E068	13663
chr15	101555976	101556180	E068	14209
chr15	101563568	101564795	E068	21801
chr15	101586174	101586250	E068	44407
chr15	101586290	101586340	E068	44523
chr15	101587051	101587164	E068	45284
chr15	101563568	101564795	E069	21801
chr15	101555430	101555954	E070	13663
chr15	101555976	101556180	E070	14209
chr15	101547090	101548240	E071	5323
chr15	101555163	101555330	E071	13396
chr15	101555430	101555954	E071	13663
chr15	101563265	101563340	E071	21498
chr15	101563568	101564795	E071	21801
chr15	101555430	101555954	E072	13663
chr15	101555976	101556180	E072	14209
chr15	101555163	101555330	E073	13396
chr15	101555430	101555954	E073	13663
chr15	101555976	101556180	E073	14209
chr15	101561022	101561376	E073	19255
chr15	101561509	101561604	E073	19742
chr15	101563568	101564795	E073	21801
chr15	101564915	101565077	E073	23148
chr15	101547090	101548240	E074	5323
chr15	101555430	101555954	E081	13663
chr15	101588497	101588703	E081	46730
chr15	101553949	101554038	E082	12182
chr15	101554162	101554493	E082	12395

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr15	101513539	101513651	E067	-28116
chr15	101513653	101513845	E067	-27922
chr15	101513867	101513982	E067	-27785
chr15	101514052	101514409	E067	-27358
chr15	101548384	101549338	E067	6617
chr15	101513279	101513522	E068	-28245
chr15	101513539	101513651	E068	-28116
chr15	101513653	101513845	E068	-27922
chr15	101513867	101513982	E068	-27785
chr15	101548384	101549338	E068	6617
chr15	101513539	101513651	E069	-28116
chr15	101513653	101513845	E069	-27922
chr15	101513867	101513982	E069	-27785
chr15	101548384	101549338	E069	6617
chr15	101548384	101549338	E070	6617
chr15	101513279	101513522	E071	-28245
chr15	101513539	101513651	E071	-28116
chr15	101513653	101513845	E071	-27922
chr15	101548384	101549338	E071	6617
chr15	101513279	101513522	E072	-28245
chr15	101513539	101513651	E072	-28116
chr15	101513653	101513845	E072	-27922
chr15	101514052	101514409	E072	-27358
chr15	101548384	101549338	E072	6617
chr15	101513279	101513522	E073	-28245
chr15	101513539	101513651	E073	-28116
chr15	101513653	101513845	E073	-27922
chr15	101513867	101513982	E073	-27785
chr15	101514052	101514409	E073	-27358
chr15	101548384	101549338	E073	6617
chr15	101513867	101513982	E074	-27785
chr15	101548384	101549338	E082	6617