rs1579695

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0426 (12766/29926,GnomAD)
A=0435 (12684/29118,TOPMED)
A=0416 (2081/5008,1000G)
G==0487 (1876/3854,ALSPAC)
G==0495 (1837/3708,TWINSUK)

Position: chr2:198035639 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 134 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.198035639G>A
GRCh37.p13 chr 2	NC_000002.11:g.198900363G>A

Gene: PLCL1, phospholipase C like 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLCL1 transcript	NM_006226.3:c.	N/A	Intron Variant
PLCL1 transcript variant X1	XM_005246643.3:c.	N/A	Intron Variant
PLCL1 transcript variant X3	XM_011511351.2:c.	N/A	Intron Variant
PLCL1 transcript variant X2	XM_017004339.1:c.	N/A	Intron Variant
PLCL1 transcript variant X5	XM_017004340.1:c.	N/A	Intron Variant
PLCL1 transcript variant X4	XM_005246644.3:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.659	A=0.341
1000Genomes	American	Sub	694	G=0.580	A=0.420
1000Genomes	East Asian	Sub	1008	G=0.779	A=0.221
1000Genomes	Europe	Sub	1006	G=0.450	A=0.550
1000Genomes	Global	Study-wide	5008	G=0.584	A=0.416
1000Genomes	South Asian	Sub	978	G=0.420	A=0.580
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.487	A=0.513
The Genome Aggregation Database	African	Sub	8710	G=0.637	A=0.363
The Genome Aggregation Database	American	Sub	836	G=0.660	A=0.340
The Genome Aggregation Database	East Asian	Sub	1616	G=0.801	A=0.199
The Genome Aggregation Database	Europe	Sub	18462	G=0.521	A=0.478
The Genome Aggregation Database	Global	Study-wide	29926	G=0.573	A=0.426
The Genome Aggregation Database	Other	Sub	302	G=0.480	A=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.564	A=0.435
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.495	A=0.505

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs1579695	1.12E-05	alcohol consumption	23743675

eQTL of rs1579695 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 rs1579695 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	198859584	198859710	E067	-40653
chr2	198860594	198860652	E067	-39711
chr2	198861601	198861700	E067	-38663
chr2	198861897	198861982	E067	-38381
chr2	198862039	198862206	E067	-38157
chr2	198862262	198862312	E067	-38051
chr2	198863014	198863054	E067	-37309
chr2	198895311	198895383	E067	-4980
chr2	198905291	198905433	E067	4928
chr2	198918578	198918696	E067	18215
chr2	198945273	198945529	E067	44910
chr2	198860594	198860652	E068	-39711
chr2	198861601	198861700	E068	-38663
chr2	198861897	198861982	E068	-38381
chr2	198869628	198869727	E068	-30636
chr2	198869765	198869846	E068	-30517
chr2	198894292	198894356	E068	-6007
chr2	198905291	198905433	E068	4928
chr2	198905500	198905702	E068	5137
chr2	198919509	198919737	E068	19146
chr2	198919820	198920207	E068	19457
chr2	198920560	198920776	E068	20197
chr2	198922587	198922655	E068	22224
chr2	198930117	198930438	E068	29754
chr2	198945273	198945529	E068	44910
chr2	198860594	198860652	E069	-39711
chr2	198861601	198861700	E069	-38663
chr2	198869765	198869846	E069	-30517
chr2	198870058	198870605	E069	-29758
chr2	198881929	198882001	E069	-18362
chr2	198895156	198895261	E069	-5102
chr2	198895311	198895383	E069	-4980
chr2	198895428	198895521	E069	-4842
chr2	198902752	198902963	E069	2389
chr2	198905291	198905433	E069	4928
chr2	198905500	198905702	E069	5137
chr2	198906774	198907233	E069	6411
chr2	198917564	198917745	E069	17201
chr2	198917974	198918065	E069	17611
chr2	198918578	198918696	E069	18215
chr2	198930117	198930438	E069	29754
chr2	198945273	198945529	E069	44910
chr2	198894809	198894947	E070	-5416
chr2	198896952	198897006	E070	-3357
chr2	198898314	198898364	E070	-1999
chr2	198920560	198920776	E070	20197
chr2	198858638	198858821	E071	-41542
chr2	198860594	198860652	E071	-39711
chr2	198861601	198861700	E071	-38663
chr2	198861897	198861982	E071	-38381
chr2	198862039	198862206	E071	-38157
chr2	198862262	198862312	E071	-38051
chr2	198869003	198869098	E071	-31265
chr2	198869628	198869727	E071	-30636
chr2	198869765	198869846	E071	-30517
chr2	198894292	198894356	E071	-6007
chr2	198894442	198894522	E071	-5841
chr2	198894809	198894947	E071	-5416
chr2	198902752	198902963	E071	2389
chr2	198903313	198903359	E071	2950
chr2	198905291	198905433	E071	4928
chr2	198905500	198905702	E071	5137
chr2	198906774	198907233	E071	6411
chr2	198917564	198917745	E071	17201
chr2	198917974	198918065	E071	17611
chr2	198918578	198918696	E071	18215
chr2	198919150	198919308	E071	18787
chr2	198919509	198919737	E071	19146
chr2	198919820	198920207	E071	19457
chr2	198920560	198920776	E071	20197
chr2	198925168	198925266	E071	24805
chr2	198930117	198930438	E071	29754
chr2	198931481	198931548	E071	31118
chr2	198945273	198945529	E071	44910
chr2	198860594	198860652	E072	-39711
chr2	198861601	198861700	E072	-38663
chr2	198861897	198861982	E072	-38381
chr2	198862039	198862206	E072	-38157
chr2	198862262	198862312	E072	-38051
chr2	198870058	198870605	E072	-29758
chr2	198881929	198882001	E072	-18362
chr2	198895428	198895521	E072	-4842
chr2	198902752	198902963	E072	2389
chr2	198905291	198905433	E072	4928
chr2	198905500	198905702	E072	5137
chr2	198914419	198914505	E072	14056
chr2	198917974	198918065	E072	17611
chr2	198918578	198918696	E072	18215
chr2	198919150	198919308	E072	18787
chr2	198919509	198919737	E072	19146
chr2	198919820	198920207	E072	19457
chr2	198920560	198920776	E072	20197
chr2	198922587	198922655	E072	22224
chr2	198925168	198925266	E072	24805
chr2	198945273	198945529	E072	44910
chr2	198860594	198860652	E073	-39711
chr2	198861601	198861700	E073	-38663
chr2	198869628	198869727	E073	-30636
chr2	198869765	198869846	E073	-30517
chr2	198870058	198870605	E073	-29758
chr2	198918578	198918696	E073	18215
chr2	198919150	198919308	E073	18787
chr2	198919509	198919737	E073	19146
chr2	198860594	198860652	E074	-39711
chr2	198861601	198861700	E074	-38663
chr2	198861897	198861982	E074	-38381
chr2	198862039	198862206	E074	-38157
chr2	198862262	198862312	E074	-38051
chr2	198863014	198863054	E074	-37309
chr2	198868844	198868923	E074	-31440
chr2	198869003	198869098	E074	-31265
chr2	198869628	198869727	E074	-30636
chr2	198869765	198869846	E074	-30517
chr2	198881929	198882001	E074	-18362
chr2	198894292	198894356	E074	-6007
chr2	198894442	198894522	E074	-5841
chr2	198894809	198894947	E074	-5416
chr2	198895156	198895261	E074	-5102
chr2	198895311	198895383	E074	-4980
chr2	198902752	198902963	E074	2389
chr2	198905291	198905433	E074	4928
chr2	198905500	198905702	E074	5137
chr2	198906774	198907233	E074	6411
chr2	198917564	198917745	E074	17201
chr2	198917974	198918065	E074	17611
chr2	198918578	198918696	E074	18215
chr2	198919150	198919308	E074	18787
chr2	198919509	198919737	E074	19146
chr2	198919820	198920207	E074	19457
chr2	198920560	198920776	E074	20197
chr2	198930117	198930438	E074	29754
chr2	198931481	198931548	E074	31118
chr2	198945273	198945529	E074	44910
chr2	198945273	198945529	E081	44910