rs1595823

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0463 (13868/29918,GnomAD)
T=0491 (14303/29118,TOPMED)
T=0450 (2255/5008,1000G)
C==0494 (1905/3854,ALSPAC)
T=0496 (1841/3708,TWINSUK)

Position: chr2:198027075 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 133 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.198027075C>T
GRCh37.p13 chr 2	NC_000002.11:g.198891799C>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=0.503	T=0.497
1000Genomes	American	Sub	694	C=0.580	T=0.420
1000Genomes	East Asian	Sub	1008	C=0.780	T=0.220
1000Genomes	Europe	Sub	1006	C=0.454	T=0.546
1000Genomes	Global	Study-wide	5008	C=0.550	T=0.450
1000Genomes	South Asian	Sub	978	C=0.450	T=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.494	T=0.506
The Genome Aggregation Database	African	Sub	8688	C=0.493	T=0.507
The Genome Aggregation Database	American	Sub	834	C=0.660	T=0.340
The Genome Aggregation Database	East Asian	Sub	1622	C=0.802	T=0.198
The Genome Aggregation Database	Europe	Sub	18472	C=0.529	T=0.471
The Genome Aggregation Database	Global	Study-wide	29918	C=0.536	T=0.463
The Genome Aggregation Database	Other	Sub	302	C=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.508	T=0.491
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.504	T=0.496

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
rs1595823	1.62E-05	alcohol consumption	23743675

eQTL of rs1595823 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:198891799	SF3B1	ENSG00000115524.11	C>T	7.6222e-4	591984	Caudate_basal_ganglia

meQTL of rs1595823 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	198849914	198850263	E067	-41536
chr2	198859584	198859710	E067	-32089
chr2	198860594	198860652	E067	-31147
chr2	198861601	198861700	E067	-30099
chr2	198861897	198861982	E067	-29817
chr2	198862039	198862206	E067	-29593
chr2	198862262	198862312	E067	-29487
chr2	198863014	198863054	E067	-28745
chr2	198895311	198895383	E067	3512
chr2	198905291	198905433	E067	13492
chr2	198918578	198918696	E067	26779
chr2	198860594	198860652	E068	-31147
chr2	198861601	198861700	E068	-30099
chr2	198861897	198861982	E068	-29817
chr2	198869628	198869727	E068	-22072
chr2	198869765	198869846	E068	-21953
chr2	198894292	198894356	E068	2493
chr2	198905291	198905433	E068	13492
chr2	198905500	198905702	E068	13701
chr2	198919509	198919737	E068	27710
chr2	198919820	198920207	E068	28021
chr2	198920560	198920776	E068	28761
chr2	198922587	198922655	E068	30788
chr2	198930117	198930438	E068	38318
chr2	198849914	198850263	E069	-41536
chr2	198860594	198860652	E069	-31147
chr2	198861601	198861700	E069	-30099
chr2	198869765	198869846	E069	-21953
chr2	198870058	198870605	E069	-21194
chr2	198881929	198882001	E069	-9798
chr2	198895156	198895261	E069	3357
chr2	198895311	198895383	E069	3512
chr2	198895428	198895521	E069	3629
chr2	198902752	198902963	E069	10953
chr2	198905291	198905433	E069	13492
chr2	198905500	198905702	E069	13701
chr2	198906774	198907233	E069	14975
chr2	198917564	198917745	E069	25765
chr2	198917974	198918065	E069	26175
chr2	198918578	198918696	E069	26779
chr2	198930117	198930438	E069	38318
chr2	198894809	198894947	E070	3010
chr2	198896952	198897006	E070	5153
chr2	198898314	198898364	E070	6515
chr2	198920560	198920776	E070	28761
chr2	198849914	198850263	E071	-41536
chr2	198858638	198858821	E071	-32978
chr2	198860594	198860652	E071	-31147
chr2	198861601	198861700	E071	-30099
chr2	198861897	198861982	E071	-29817
chr2	198862039	198862206	E071	-29593
chr2	198862262	198862312	E071	-29487
chr2	198869003	198869098	E071	-22701
chr2	198869628	198869727	E071	-22072
chr2	198869765	198869846	E071	-21953
chr2	198894292	198894356	E071	2493
chr2	198894442	198894522	E071	2643
chr2	198894809	198894947	E071	3010
chr2	198902752	198902963	E071	10953
chr2	198903313	198903359	E071	11514
chr2	198905291	198905433	E071	13492
chr2	198905500	198905702	E071	13701
chr2	198906774	198907233	E071	14975
chr2	198917564	198917745	E071	25765
chr2	198917974	198918065	E071	26175
chr2	198918578	198918696	E071	26779
chr2	198919150	198919308	E071	27351
chr2	198919509	198919737	E071	27710
chr2	198919820	198920207	E071	28021
chr2	198920560	198920776	E071	28761
chr2	198925168	198925266	E071	33369
chr2	198930117	198930438	E071	38318
chr2	198931481	198931548	E071	39682
chr2	198849914	198850263	E072	-41536
chr2	198860594	198860652	E072	-31147
chr2	198861601	198861700	E072	-30099
chr2	198861897	198861982	E072	-29817
chr2	198862039	198862206	E072	-29593
chr2	198862262	198862312	E072	-29487
chr2	198870058	198870605	E072	-21194
chr2	198881929	198882001	E072	-9798
chr2	198895428	198895521	E072	3629
chr2	198902752	198902963	E072	10953
chr2	198905291	198905433	E072	13492
chr2	198905500	198905702	E072	13701
chr2	198914419	198914505	E072	22620
chr2	198917974	198918065	E072	26175
chr2	198918578	198918696	E072	26779
chr2	198919150	198919308	E072	27351
chr2	198919509	198919737	E072	27710
chr2	198919820	198920207	E072	28021
chr2	198920560	198920776	E072	28761
chr2	198922587	198922655	E072	30788
chr2	198925168	198925266	E072	33369
chr2	198860594	198860652	E073	-31147
chr2	198861601	198861700	E073	-30099
chr2	198869628	198869727	E073	-22072
chr2	198869765	198869846	E073	-21953
chr2	198870058	198870605	E073	-21194
chr2	198918578	198918696	E073	26779
chr2	198919150	198919308	E073	27351
chr2	198919509	198919737	E073	27710
chr2	198849914	198850263	E074	-41536
chr2	198860594	198860652	E074	-31147
chr2	198861601	198861700	E074	-30099
chr2	198861897	198861982	E074	-29817
chr2	198862039	198862206	E074	-29593
chr2	198862262	198862312	E074	-29487
chr2	198863014	198863054	E074	-28745
chr2	198868844	198868923	E074	-22876
chr2	198869003	198869098	E074	-22701
chr2	198869628	198869727	E074	-22072
chr2	198869765	198869846	E074	-21953
chr2	198881929	198882001	E074	-9798
chr2	198894292	198894356	E074	2493
chr2	198894442	198894522	E074	2643
chr2	198894809	198894947	E074	3010
chr2	198895156	198895261	E074	3357
chr2	198895311	198895383	E074	3512
chr2	198902752	198902963	E074	10953
chr2	198905291	198905433	E074	13492
chr2	198905500	198905702	E074	13701
chr2	198906774	198907233	E074	14975
chr2	198917564	198917745	E074	25765
chr2	198917974	198918065	E074	26175
chr2	198918578	198918696	E074	26779
chr2	198919150	198919308	E074	27351
chr2	198919509	198919737	E074	27710
chr2	198919820	198920207	E074	28021
chr2	198920560	198920776	E074	28761
chr2	198930117	198930438	E074	38318
chr2	198931481	198931548	E074	39682
chr2	198849914	198850263	E082	-41536