rs1371664

Organism: Homo sapiens

Alleles: T>A

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0426 (12737/29892,GnomAD)
A=0435 (12687/29118,TOPMED)
A=0416 (2081/5008,1000G)
T==0487 (1878/3854,ALSPAC)
T==0496 (1840/3708,TWINSUK)

Position: chr2:198039741 (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.198039741T>A
GRCh37.p13 chr 2	NC_000002.11:g.198904465T>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	T=0.659	A=0.341
1000Genomes	American	Sub	694	T=0.580	A=0.420
1000Genomes	East Asian	Sub	1008	T=0.779	A=0.221
1000Genomes	Europe	Sub	1006	T=0.449	A=0.551
1000Genomes	Global	Study-wide	5008	T=0.584	A=0.416
1000Genomes	South Asian	Sub	978	T=0.430	A=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.487	A=0.513
The Genome Aggregation Database	African	Sub	8700	T=0.637	A=0.363
The Genome Aggregation Database	American	Sub	836	T=0.660	A=0.340
The Genome Aggregation Database	East Asian	Sub	1614	T=0.801	A=0.199
The Genome Aggregation Database	Europe	Sub	18440	T=0.521	A=0.478
The Genome Aggregation Database	Global	Study-wide	29892	T=0.573	A=0.426
The Genome Aggregation Database	Other	Sub	302	T=0.480	A=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.564	A=0.435
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.496	A=0.504

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
rs1371664	5.61E-06	alcohol consumption	23743675

eQTL of rs1371664 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 rs1371664 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	-44755
chr2	198860594	198860652	E067	-43813
chr2	198861601	198861700	E067	-42765
chr2	198861897	198861982	E067	-42483
chr2	198862039	198862206	E067	-42259
chr2	198862262	198862312	E067	-42153
chr2	198863014	198863054	E067	-41411
chr2	198895311	198895383	E067	-9082
chr2	198905291	198905433	E067	826
chr2	198918578	198918696	E067	14113
chr2	198945273	198945529	E067	40808
chr2	198860594	198860652	E068	-43813
chr2	198861601	198861700	E068	-42765
chr2	198861897	198861982	E068	-42483
chr2	198869628	198869727	E068	-34738
chr2	198869765	198869846	E068	-34619
chr2	198894292	198894356	E068	-10109
chr2	198905291	198905433	E068	826
chr2	198905500	198905702	E068	1035
chr2	198919509	198919737	E068	15044
chr2	198919820	198920207	E068	15355
chr2	198920560	198920776	E068	16095
chr2	198922587	198922655	E068	18122
chr2	198930117	198930438	E068	25652
chr2	198945273	198945529	E068	40808
chr2	198860594	198860652	E069	-43813
chr2	198861601	198861700	E069	-42765
chr2	198869765	198869846	E069	-34619
chr2	198870058	198870605	E069	-33860
chr2	198881929	198882001	E069	-22464
chr2	198895156	198895261	E069	-9204
chr2	198895311	198895383	E069	-9082
chr2	198895428	198895521	E069	-8944
chr2	198902752	198902963	E069	-1502
chr2	198905291	198905433	E069	826
chr2	198905500	198905702	E069	1035
chr2	198906774	198907233	E069	2309
chr2	198917564	198917745	E069	13099
chr2	198917974	198918065	E069	13509
chr2	198918578	198918696	E069	14113
chr2	198930117	198930438	E069	25652
chr2	198945273	198945529	E069	40808
chr2	198894809	198894947	E070	-9518
chr2	198896952	198897006	E070	-7459
chr2	198898314	198898364	E070	-6101
chr2	198920560	198920776	E070	16095
chr2	198858638	198858821	E071	-45644
chr2	198860594	198860652	E071	-43813
chr2	198861601	198861700	E071	-42765
chr2	198861897	198861982	E071	-42483
chr2	198862039	198862206	E071	-42259
chr2	198862262	198862312	E071	-42153
chr2	198869003	198869098	E071	-35367
chr2	198869628	198869727	E071	-34738
chr2	198869765	198869846	E071	-34619
chr2	198894292	198894356	E071	-10109
chr2	198894442	198894522	E071	-9943
chr2	198894809	198894947	E071	-9518
chr2	198902752	198902963	E071	-1502
chr2	198903313	198903359	E071	-1106
chr2	198905291	198905433	E071	826
chr2	198905500	198905702	E071	1035
chr2	198906774	198907233	E071	2309
chr2	198917564	198917745	E071	13099
chr2	198917974	198918065	E071	13509
chr2	198918578	198918696	E071	14113
chr2	198919150	198919308	E071	14685
chr2	198919509	198919737	E071	15044
chr2	198919820	198920207	E071	15355
chr2	198920560	198920776	E071	16095
chr2	198925168	198925266	E071	20703
chr2	198930117	198930438	E071	25652
chr2	198931481	198931548	E071	27016
chr2	198945273	198945529	E071	40808
chr2	198860594	198860652	E072	-43813
chr2	198861601	198861700	E072	-42765
chr2	198861897	198861982	E072	-42483
chr2	198862039	198862206	E072	-42259
chr2	198862262	198862312	E072	-42153
chr2	198870058	198870605	E072	-33860
chr2	198881929	198882001	E072	-22464
chr2	198895428	198895521	E072	-8944
chr2	198902752	198902963	E072	-1502
chr2	198905291	198905433	E072	826
chr2	198905500	198905702	E072	1035
chr2	198914419	198914505	E072	9954
chr2	198917974	198918065	E072	13509
chr2	198918578	198918696	E072	14113
chr2	198919150	198919308	E072	14685
chr2	198919509	198919737	E072	15044
chr2	198919820	198920207	E072	15355
chr2	198920560	198920776	E072	16095
chr2	198922587	198922655	E072	18122
chr2	198925168	198925266	E072	20703
chr2	198945273	198945529	E072	40808
chr2	198860594	198860652	E073	-43813
chr2	198861601	198861700	E073	-42765
chr2	198869628	198869727	E073	-34738
chr2	198869765	198869846	E073	-34619
chr2	198870058	198870605	E073	-33860
chr2	198918578	198918696	E073	14113
chr2	198919150	198919308	E073	14685
chr2	198919509	198919737	E073	15044
chr2	198860594	198860652	E074	-43813
chr2	198861601	198861700	E074	-42765
chr2	198861897	198861982	E074	-42483
chr2	198862039	198862206	E074	-42259
chr2	198862262	198862312	E074	-42153
chr2	198863014	198863054	E074	-41411
chr2	198868844	198868923	E074	-35542
chr2	198869003	198869098	E074	-35367
chr2	198869628	198869727	E074	-34738
chr2	198869765	198869846	E074	-34619
chr2	198881929	198882001	E074	-22464
chr2	198894292	198894356	E074	-10109
chr2	198894442	198894522	E074	-9943
chr2	198894809	198894947	E074	-9518
chr2	198895156	198895261	E074	-9204
chr2	198895311	198895383	E074	-9082
chr2	198902752	198902963	E074	-1502
chr2	198905291	198905433	E074	826
chr2	198905500	198905702	E074	1035
chr2	198906774	198907233	E074	2309
chr2	198917564	198917745	E074	13099
chr2	198917974	198918065	E074	13509
chr2	198918578	198918696	E074	14113
chr2	198919150	198919308	E074	14685
chr2	198919509	198919737	E074	15044
chr2	198919820	198920207	E074	15355
chr2	198920560	198920776	E074	16095
chr2	198930117	198930438	E074	25652
chr2	198931481	198931548	E074	27016
chr2	198945273	198945529	E074	40808
chr2	198945273	198945529	E081	40808