rs6719289

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PLB1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0329 (9846/29898,GnomAD)
G=0330 (9608/29116,TOPMED)
G=0294 (1470/5008,1000G)
G=0353 (1362/3854,ALSPAC)
G=0370 (1373/3708,TWINSUK)

Position: chr2:28633935 (GRCh38.p7) (2p23.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 122 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.28633935A>G
GRCh37.p13 chr 2	NC_000002.11:g.28856801A>G

Gene: PLB1, phospholipase B1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLB1 transcript variant 2	NM_001170585.1:c.	N/A	Intron Variant
PLB1 transcript variant 1	NM_153021.4:c.	N/A	Intron Variant
PLB1 transcript variant X2	XM_011532579.2:c.	N/A	Intron Variant
PLB1 transcript variant X4	XM_011532581.2:c.	N/A	Intron Variant
PLB1 transcript variant X8	XM_011532588.2:c.	N/A	Intron Variant
PLB1 transcript variant X1	XM_011532589.2:c.	N/A	Intron Variant
PLB1 transcript variant X10	XM_011532591.2:c.	N/A	Intron Variant
PLB1 transcript variant X7	XM_011532593.2:c.	N/A	Intron Variant
PLB1 transcript variant X14	XM_011532601.2:c.	N/A	Intron Variant
PLB1 transcript variant X16	XM_011532602.2:c.	N/A	Intron Variant
PLB1 transcript variant X15	XM_011532603.2:c.	N/A	Intron Variant
PLB1 transcript variant X20	XM_011532609.2:c.	N/A	Intron Variant
PLB1 transcript variant X21	XM_011532610.2:c.	N/A	Intron Variant
PLB1 transcript variant X3	XM_017003432.1:c.	N/A	Intron Variant
PLB1 transcript variant X5	XM_017003433.1:c.	N/A	Intron Variant
PLB1 transcript variant X6	XM_011532584.2:c.	N/A	Genic Downstream Transcript Variant
PLB1 transcript variant X9	XM_011532590.2:c.	N/A	Genic Downstream Transcript Variant
PLB1 transcript variant X18	XM_011532606.2:c.	N/A	Genic Downstream Transcript Variant
PLB1 transcript variant X19	XM_011532607.2:c.	N/A	Genic Downstream Transcript Variant
PLB1 transcript variant X22	XM_011532608.2:c.	N/A	Genic Downstream Transcript Variant
PLB1 transcript variant X11	XM_017003434.1:c.	N/A	Genic Downstream Transcript Variant
PLB1 transcript variant X13	XR_001738646.1:n.	N/A	Intron Variant
PLB1 transcript variant X17	XR_001738647.1:n.	N/A	Genic Downstream Transcript Variant
PLB1 transcript variant X12	XR_939663.2:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.759	G=0.241
1000Genomes	American	Sub	694	A=0.770	G=0.230
1000Genomes	East Asian	Sub	1008	A=0.679	G=0.321
1000Genomes	Europe	Sub	1006	A=0.629	G=0.371
1000Genomes	Global	Study-wide	5008	A=0.706	G=0.294
1000Genomes	South Asian	Sub	978	A=0.700	G=0.300
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.647	G=0.353
The Genome Aggregation Database	African	Sub	8696	A=0.728	G=0.272
The Genome Aggregation Database	American	Sub	836	A=0.750	G=0.250
The Genome Aggregation Database	East Asian	Sub	1612	A=0.617	G=0.383
The Genome Aggregation Database	Europe	Sub	18452	A=0.644	G=0.355
The Genome Aggregation Database	Global	Study-wide	29898	A=0.670	G=0.329
The Genome Aggregation Database	Other	Sub	302	A=0.670	G=0.330
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.670	G=0.330
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.630	G=0.370

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
rs6719289	0.000282	nicotine smoking	19268276

eQTL of rs6719289 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 rs6719289 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 )
chr2	28810497	28811513	E067	-45288
chr2	28816876	28818270	E067	-38531
chr2	28830639	28830712	E067	-26089
chr2	28830742	28830861	E067	-25940
chr2	28843402	28843483	E067	-13318
chr2	28843538	28843768	E067	-13033
chr2	28843786	28843852	E067	-12949
chr2	28843890	28845243	E067	-11558
chr2	28847467	28848802	E067	-7999
chr2	28886964	28887596	E067	30163
chr2	28887639	28887749	E067	30838
chr2	28887836	28888536	E067	31035
chr2	28904870	28904962	E067	48069
chr2	28809822	28810193	E068	-46608
chr2	28810497	28811513	E068	-45288
chr2	28816876	28818270	E068	-38531
chr2	28843118	28843382	E068	-13419
chr2	28843402	28843483	E068	-13318
chr2	28843538	28843768	E068	-13033
chr2	28843786	28843852	E068	-12949
chr2	28845251	28845377	E068	-11424
chr2	28845423	28845528	E068	-11273
chr2	28847467	28848802	E068	-7999
chr2	28857837	28858630	E068	1036
chr2	28858777	28858835	E068	1976
chr2	28886237	28886642	E068	29436
chr2	28886803	28886873	E068	30002
chr2	28886964	28887596	E068	30163
chr2	28887639	28887749	E068	30838
chr2	28887836	28888536	E068	31035
chr2	28893631	28894100	E068	36830
chr2	28903602	28903860	E068	46801
chr2	28829722	28830527	E069	-26274
chr2	28830639	28830712	E069	-26089
chr2	28830742	28830861	E069	-25940
chr2	28843118	28843382	E069	-13419
chr2	28843402	28843483	E069	-13318
chr2	28843538	28843768	E069	-13033
chr2	28843786	28843852	E069	-12949
chr2	28843890	28845243	E069	-11558
chr2	28886964	28887596	E069	30163
chr2	28887639	28887749	E069	30838
chr2	28887836	28888536	E069	31035
chr2	28866304	28866530	E070	9503
chr2	28886803	28886873	E070	30002
chr2	28886964	28887596	E070	30163
chr2	28887639	28887749	E070	30838
chr2	28887836	28888536	E070	31035
chr2	28888682	28888751	E070	31881
chr2	28893631	28894100	E070	36830
chr2	28902768	28902848	E070	45967
chr2	28903336	28903544	E070	46535
chr2	28903602	28903860	E070	46801
chr2	28903892	28904784	E070	47091
chr2	28904870	28904962	E070	48069
chr2	28905455	28905512	E070	48654
chr2	28905520	28905570	E070	48719
chr2	28843118	28843382	E071	-13419
chr2	28843402	28843483	E071	-13318
chr2	28843538	28843768	E071	-13033
chr2	28843786	28843852	E071	-12949
chr2	28843890	28845243	E071	-11558
chr2	28847467	28848802	E071	-7999
chr2	28886803	28886873	E071	30002
chr2	28886964	28887596	E071	30163
chr2	28887639	28887749	E071	30838
chr2	28887836	28888536	E071	31035
chr2	28903336	28903544	E071	46535
chr2	28903602	28903860	E071	46801
chr2	28810497	28811513	E072	-45288
chr2	28816876	28818270	E072	-38531
chr2	28843402	28843483	E072	-13318
chr2	28843538	28843768	E072	-13033
chr2	28843786	28843852	E072	-12949
chr2	28843890	28845243	E072	-11558
chr2	28847467	28848802	E072	-7999
chr2	28856569	28857095	E072	0
chr2	28887639	28887749	E072	30838
chr2	28887836	28888536	E072	31035
chr2	28810497	28811513	E073	-45288
chr2	28816876	28818270	E073	-38531
chr2	28830639	28830712	E073	-26089
chr2	28830742	28830861	E073	-25940
chr2	28843118	28843382	E073	-13419
chr2	28843402	28843483	E073	-13318
chr2	28843538	28843768	E073	-13033
chr2	28843786	28843852	E073	-12949
chr2	28843890	28845243	E073	-11558
chr2	28847467	28848802	E073	-7999
chr2	28850484	28850630	E073	-6171
chr2	28850667	28850859	E073	-5942
chr2	28850893	28851231	E073	-5570
chr2	28857837	28858630	E073	1036
chr2	28884221	28886035	E073	27420
chr2	28886803	28886873	E073	30002
chr2	28886964	28887596	E073	30163
chr2	28887639	28887749	E073	30838
chr2	28887836	28888536	E073	31035
chr2	28816876	28818270	E074	-38531
chr2	28843118	28843382	E074	-13419
chr2	28843402	28843483	E074	-13318
chr2	28843538	28843768	E074	-13033
chr2	28843786	28843852	E074	-12949
chr2	28843890	28845243	E074	-11558
chr2	28845251	28845377	E074	-11424
chr2	28847467	28848802	E074	-7999
chr2	28852140	28852278	E074	-4523
chr2	28886964	28887596	E074	30163
chr2	28887836	28888536	E074	31035
chr2	28829722	28830527	E081	-26274
chr2	28830639	28830712	E081	-26089
chr2	28830742	28830861	E081	-25940
chr2	28830915	28831589	E081	-25212
chr2	28903602	28903860	E081	46801
chr2	28903892	28904784	E081	47091
chr2	28904870	28904962	E081	48069
chr2	28829722	28830527	E082	-26274
chr2	28830639	28830712	E082	-26089
chr2	28830742	28830861	E082	-25940
chr2	28830915	28831589	E082	-25212
chr2	28843890	28845243	E082	-11558
chr2	28887836	28888536	E082	31035