rs1583792

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0469 (14032/29912,GnomAD)
C==0498 (14500/29118,TOPMED)
T=0464 (2324/5008,1000G)
C==0486 (1874/3854,ALSPAC)
C==0495 (1835/3708,TWINSUK)

Position: chr2:198035564 (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.198035564C>T
GRCh37.p13 chr 2	NC_000002.11:g.198900288C>T

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	C=0.481	T=0.519
1000Genomes	American	Sub	694	C=0.570	T=0.430
1000Genomes	East Asian	Sub	1008	C=0.779	T=0.221
1000Genomes	Europe	Sub	1006	C=0.449	T=0.551
1000Genomes	Global	Study-wide	5008	C=0.536	T=0.464
1000Genomes	South Asian	Sub	978	C=0.430	T=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.486	T=0.514
The Genome Aggregation Database	African	Sub	8704	C=0.493	T=0.507
The Genome Aggregation Database	American	Sub	832	C=0.650	T=0.350
The Genome Aggregation Database	East Asian	Sub	1614	C=0.802	T=0.198
The Genome Aggregation Database	Europe	Sub	18460	C=0.520	T=0.479
The Genome Aggregation Database	Global	Study-wide	29912	C=0.530	T=0.469
The Genome Aggregation Database	Other	Sub	302	C=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.498	T=0.502
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.495	T=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
rs1583792	7.26E-06	alcohol consumption	23743675

eQTL of rs1583792 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 rs1583792 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	-40578
chr2	198860594	198860652	E067	-39636
chr2	198861601	198861700	E067	-38588
chr2	198861897	198861982	E067	-38306
chr2	198862039	198862206	E067	-38082
chr2	198862262	198862312	E067	-37976
chr2	198863014	198863054	E067	-37234
chr2	198895311	198895383	E067	-4905
chr2	198905291	198905433	E067	5003
chr2	198918578	198918696	E067	18290
chr2	198945273	198945529	E067	44985
chr2	198860594	198860652	E068	-39636
chr2	198861601	198861700	E068	-38588
chr2	198861897	198861982	E068	-38306
chr2	198869628	198869727	E068	-30561
chr2	198869765	198869846	E068	-30442
chr2	198894292	198894356	E068	-5932
chr2	198905291	198905433	E068	5003
chr2	198905500	198905702	E068	5212
chr2	198919509	198919737	E068	19221
chr2	198919820	198920207	E068	19532
chr2	198920560	198920776	E068	20272
chr2	198922587	198922655	E068	22299
chr2	198930117	198930438	E068	29829
chr2	198945273	198945529	E068	44985
chr2	198860594	198860652	E069	-39636
chr2	198861601	198861700	E069	-38588
chr2	198869765	198869846	E069	-30442
chr2	198870058	198870605	E069	-29683
chr2	198881929	198882001	E069	-18287
chr2	198895156	198895261	E069	-5027
chr2	198895311	198895383	E069	-4905
chr2	198895428	198895521	E069	-4767
chr2	198902752	198902963	E069	2464
chr2	198905291	198905433	E069	5003
chr2	198905500	198905702	E069	5212
chr2	198906774	198907233	E069	6486
chr2	198917564	198917745	E069	17276
chr2	198917974	198918065	E069	17686
chr2	198918578	198918696	E069	18290
chr2	198930117	198930438	E069	29829
chr2	198945273	198945529	E069	44985
chr2	198894809	198894947	E070	-5341
chr2	198896952	198897006	E070	-3282
chr2	198898314	198898364	E070	-1924
chr2	198920560	198920776	E070	20272
chr2	198858638	198858821	E071	-41467
chr2	198860594	198860652	E071	-39636
chr2	198861601	198861700	E071	-38588
chr2	198861897	198861982	E071	-38306
chr2	198862039	198862206	E071	-38082
chr2	198862262	198862312	E071	-37976
chr2	198869003	198869098	E071	-31190
chr2	198869628	198869727	E071	-30561
chr2	198869765	198869846	E071	-30442
chr2	198894292	198894356	E071	-5932
chr2	198894442	198894522	E071	-5766
chr2	198894809	198894947	E071	-5341
chr2	198902752	198902963	E071	2464
chr2	198903313	198903359	E071	3025
chr2	198905291	198905433	E071	5003
chr2	198905500	198905702	E071	5212
chr2	198906774	198907233	E071	6486
chr2	198917564	198917745	E071	17276
chr2	198917974	198918065	E071	17686
chr2	198918578	198918696	E071	18290
chr2	198919150	198919308	E071	18862
chr2	198919509	198919737	E071	19221
chr2	198919820	198920207	E071	19532
chr2	198920560	198920776	E071	20272
chr2	198925168	198925266	E071	24880
chr2	198930117	198930438	E071	29829
chr2	198931481	198931548	E071	31193
chr2	198945273	198945529	E071	44985
chr2	198860594	198860652	E072	-39636
chr2	198861601	198861700	E072	-38588
chr2	198861897	198861982	E072	-38306
chr2	198862039	198862206	E072	-38082
chr2	198862262	198862312	E072	-37976
chr2	198870058	198870605	E072	-29683
chr2	198881929	198882001	E072	-18287
chr2	198895428	198895521	E072	-4767
chr2	198902752	198902963	E072	2464
chr2	198905291	198905433	E072	5003
chr2	198905500	198905702	E072	5212
chr2	198914419	198914505	E072	14131
chr2	198917974	198918065	E072	17686
chr2	198918578	198918696	E072	18290
chr2	198919150	198919308	E072	18862
chr2	198919509	198919737	E072	19221
chr2	198919820	198920207	E072	19532
chr2	198920560	198920776	E072	20272
chr2	198922587	198922655	E072	22299
chr2	198925168	198925266	E072	24880
chr2	198945273	198945529	E072	44985
chr2	198860594	198860652	E073	-39636
chr2	198861601	198861700	E073	-38588
chr2	198869628	198869727	E073	-30561
chr2	198869765	198869846	E073	-30442
chr2	198870058	198870605	E073	-29683
chr2	198918578	198918696	E073	18290
chr2	198919150	198919308	E073	18862
chr2	198919509	198919737	E073	19221
chr2	198860594	198860652	E074	-39636
chr2	198861601	198861700	E074	-38588
chr2	198861897	198861982	E074	-38306
chr2	198862039	198862206	E074	-38082
chr2	198862262	198862312	E074	-37976
chr2	198863014	198863054	E074	-37234
chr2	198868844	198868923	E074	-31365
chr2	198869003	198869098	E074	-31190
chr2	198869628	198869727	E074	-30561
chr2	198869765	198869846	E074	-30442
chr2	198881929	198882001	E074	-18287
chr2	198894292	198894356	E074	-5932
chr2	198894442	198894522	E074	-5766
chr2	198894809	198894947	E074	-5341
chr2	198895156	198895261	E074	-5027
chr2	198895311	198895383	E074	-4905
chr2	198902752	198902963	E074	2464
chr2	198905291	198905433	E074	5003
chr2	198905500	198905702	E074	5212
chr2	198906774	198907233	E074	6486
chr2	198917564	198917745	E074	17276
chr2	198917974	198918065	E074	17686
chr2	198918578	198918696	E074	18290
chr2	198919150	198919308	E074	18862
chr2	198919509	198919737	E074	19221
chr2	198919820	198920207	E074	19532
chr2	198920560	198920776	E074	20272
chr2	198930117	198930438	E074	29829
chr2	198931481	198931548	E074	31193
chr2	198945273	198945529	E074	44985
chr2	198945273	198945529	E081	44985