rs962210

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0469 (14025/29888,GnomAD)
A==0497 (14497/29118,TOPMED)
T=0464 (2324/5008,1000G)
A==0488 (1879/3854,ALSPAC)
A==0496 (1838/3708,TWINSUK)

Position: chr2:198037506 (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.198037506A>T
GRCh37.p13 chr 2	NC_000002.11:g.198902230A>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	A=0.481	T=0.519
1000Genomes	American	Sub	694	A=0.570	T=0.430
1000Genomes	East Asian	Sub	1008	A=0.779	T=0.221
1000Genomes	Europe	Sub	1006	A=0.449	T=0.551
1000Genomes	Global	Study-wide	5008	A=0.536	T=0.464
1000Genomes	South Asian	Sub	978	A=0.430	T=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.488	T=0.512
The Genome Aggregation Database	African	Sub	8710	A=0.492	T=0.508
The Genome Aggregation Database	American	Sub	834	A=0.650	T=0.350
The Genome Aggregation Database	East Asian	Sub	1612	A=0.801	T=0.199
The Genome Aggregation Database	Europe	Sub	18432	A=0.520	T=0.479
The Genome Aggregation Database	Global	Study-wide	29888	A=0.530	T=0.469
The Genome Aggregation Database	Other	Sub	300	A=0.470	T=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.497	T=0.502
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.496	T=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
rs962210	6.11E-06	alcohol consumption	23743675

eQTL of rs962210 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 rs962210 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	-42520
chr2	198860594	198860652	E067	-41578
chr2	198861601	198861700	E067	-40530
chr2	198861897	198861982	E067	-40248
chr2	198862039	198862206	E067	-40024
chr2	198862262	198862312	E067	-39918
chr2	198863014	198863054	E067	-39176
chr2	198895311	198895383	E067	-6847
chr2	198905291	198905433	E067	3061
chr2	198918578	198918696	E067	16348
chr2	198945273	198945529	E067	43043
chr2	198860594	198860652	E068	-41578
chr2	198861601	198861700	E068	-40530
chr2	198861897	198861982	E068	-40248
chr2	198869628	198869727	E068	-32503
chr2	198869765	198869846	E068	-32384
chr2	198894292	198894356	E068	-7874
chr2	198905291	198905433	E068	3061
chr2	198905500	198905702	E068	3270
chr2	198919509	198919737	E068	17279
chr2	198919820	198920207	E068	17590
chr2	198920560	198920776	E068	18330
chr2	198922587	198922655	E068	20357
chr2	198930117	198930438	E068	27887
chr2	198945273	198945529	E068	43043
chr2	198860594	198860652	E069	-41578
chr2	198861601	198861700	E069	-40530
chr2	198869765	198869846	E069	-32384
chr2	198870058	198870605	E069	-31625
chr2	198881929	198882001	E069	-20229
chr2	198895156	198895261	E069	-6969
chr2	198895311	198895383	E069	-6847
chr2	198895428	198895521	E069	-6709
chr2	198902752	198902963	E069	522
chr2	198905291	198905433	E069	3061
chr2	198905500	198905702	E069	3270
chr2	198906774	198907233	E069	4544
chr2	198917564	198917745	E069	15334
chr2	198917974	198918065	E069	15744
chr2	198918578	198918696	E069	16348
chr2	198930117	198930438	E069	27887
chr2	198945273	198945529	E069	43043
chr2	198894809	198894947	E070	-7283
chr2	198896952	198897006	E070	-5224
chr2	198898314	198898364	E070	-3866
chr2	198920560	198920776	E070	18330
chr2	198858638	198858821	E071	-43409
chr2	198860594	198860652	E071	-41578
chr2	198861601	198861700	E071	-40530
chr2	198861897	198861982	E071	-40248
chr2	198862039	198862206	E071	-40024
chr2	198862262	198862312	E071	-39918
chr2	198869003	198869098	E071	-33132
chr2	198869628	198869727	E071	-32503
chr2	198869765	198869846	E071	-32384
chr2	198894292	198894356	E071	-7874
chr2	198894442	198894522	E071	-7708
chr2	198894809	198894947	E071	-7283
chr2	198902752	198902963	E071	522
chr2	198903313	198903359	E071	1083
chr2	198905291	198905433	E071	3061
chr2	198905500	198905702	E071	3270
chr2	198906774	198907233	E071	4544
chr2	198917564	198917745	E071	15334
chr2	198917974	198918065	E071	15744
chr2	198918578	198918696	E071	16348
chr2	198919150	198919308	E071	16920
chr2	198919509	198919737	E071	17279
chr2	198919820	198920207	E071	17590
chr2	198920560	198920776	E071	18330
chr2	198925168	198925266	E071	22938
chr2	198930117	198930438	E071	27887
chr2	198931481	198931548	E071	29251
chr2	198945273	198945529	E071	43043
chr2	198860594	198860652	E072	-41578
chr2	198861601	198861700	E072	-40530
chr2	198861897	198861982	E072	-40248
chr2	198862039	198862206	E072	-40024
chr2	198862262	198862312	E072	-39918
chr2	198870058	198870605	E072	-31625
chr2	198881929	198882001	E072	-20229
chr2	198895428	198895521	E072	-6709
chr2	198902752	198902963	E072	522
chr2	198905291	198905433	E072	3061
chr2	198905500	198905702	E072	3270
chr2	198914419	198914505	E072	12189
chr2	198917974	198918065	E072	15744
chr2	198918578	198918696	E072	16348
chr2	198919150	198919308	E072	16920
chr2	198919509	198919737	E072	17279
chr2	198919820	198920207	E072	17590
chr2	198920560	198920776	E072	18330
chr2	198922587	198922655	E072	20357
chr2	198925168	198925266	E072	22938
chr2	198945273	198945529	E072	43043
chr2	198860594	198860652	E073	-41578
chr2	198861601	198861700	E073	-40530
chr2	198869628	198869727	E073	-32503
chr2	198869765	198869846	E073	-32384
chr2	198870058	198870605	E073	-31625
chr2	198918578	198918696	E073	16348
chr2	198919150	198919308	E073	16920
chr2	198919509	198919737	E073	17279
chr2	198860594	198860652	E074	-41578
chr2	198861601	198861700	E074	-40530
chr2	198861897	198861982	E074	-40248
chr2	198862039	198862206	E074	-40024
chr2	198862262	198862312	E074	-39918
chr2	198863014	198863054	E074	-39176
chr2	198868844	198868923	E074	-33307
chr2	198869003	198869098	E074	-33132
chr2	198869628	198869727	E074	-32503
chr2	198869765	198869846	E074	-32384
chr2	198881929	198882001	E074	-20229
chr2	198894292	198894356	E074	-7874
chr2	198894442	198894522	E074	-7708
chr2	198894809	198894947	E074	-7283
chr2	198895156	198895261	E074	-6969
chr2	198895311	198895383	E074	-6847
chr2	198902752	198902963	E074	522
chr2	198905291	198905433	E074	3061
chr2	198905500	198905702	E074	3270
chr2	198906774	198907233	E074	4544
chr2	198917564	198917745	E074	15334
chr2	198917974	198918065	E074	15744
chr2	198918578	198918696	E074	16348
chr2	198919150	198919308	E074	16920
chr2	198919509	198919737	E074	17279
chr2	198919820	198920207	E074	17590
chr2	198920560	198920776	E074	18330
chr2	198930117	198930438	E074	27887
chr2	198931481	198931548	E074	29251
chr2	198945273	198945529	E074	43043
chr2	198945273	198945529	E081	43043