rs2196175

Organism: Homo sapiens

Alleles: T>A

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0468 (14019/29896,GnomAD)
T==0497 (14496/29118,TOPMED)
A=0464 (2324/5008,1000G)
T==0487 (1877/3854,ALSPAC)
T==0495 (1835/3708,TWINSUK)

Position: chr2:198040349 (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.198040349T>A
GRCh37.p13 chr 2	NC_000002.11:g.198905073T>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=0.481	A=0.519
1000Genomes	American	Sub	694	T=0.570	A=0.430
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=0.536	A=0.464
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	8694	T=0.493	A=0.507
The Genome Aggregation Database	American	Sub	834	T=0.650	A=0.350
The Genome Aggregation Database	East Asian	Sub	1612	T=0.803	A=0.197
The Genome Aggregation Database	Europe	Sub	18454	T=0.521	A=0.479
The Genome Aggregation Database	Global	Study-wide	29896	T=0.531	A=0.468
The Genome Aggregation Database	Other	Sub	302	T=0.480	A=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.497	A=0.502
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=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
rs2196175	6.98E-06	alcohol consumption	23743675

eQTL of rs2196175 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 rs2196175 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	-45363
chr2	198860594	198860652	E067	-44421
chr2	198861601	198861700	E067	-43373
chr2	198861897	198861982	E067	-43091
chr2	198862039	198862206	E067	-42867
chr2	198862262	198862312	E067	-42761
chr2	198863014	198863054	E067	-42019
chr2	198895311	198895383	E067	-9690
chr2	198905291	198905433	E067	218
chr2	198918578	198918696	E067	13505
chr2	198945273	198945529	E067	40200
chr2	198860594	198860652	E068	-44421
chr2	198861601	198861700	E068	-43373
chr2	198861897	198861982	E068	-43091
chr2	198869628	198869727	E068	-35346
chr2	198869765	198869846	E068	-35227
chr2	198894292	198894356	E068	-10717
chr2	198905291	198905433	E068	218
chr2	198905500	198905702	E068	427
chr2	198919509	198919737	E068	14436
chr2	198919820	198920207	E068	14747
chr2	198920560	198920776	E068	15487
chr2	198922587	198922655	E068	17514
chr2	198930117	198930438	E068	25044
chr2	198945273	198945529	E068	40200
chr2	198860594	198860652	E069	-44421
chr2	198861601	198861700	E069	-43373
chr2	198869765	198869846	E069	-35227
chr2	198870058	198870605	E069	-34468
chr2	198881929	198882001	E069	-23072
chr2	198895156	198895261	E069	-9812
chr2	198895311	198895383	E069	-9690
chr2	198895428	198895521	E069	-9552
chr2	198902752	198902963	E069	-2110
chr2	198905291	198905433	E069	218
chr2	198905500	198905702	E069	427
chr2	198906774	198907233	E069	1701
chr2	198917564	198917745	E069	12491
chr2	198917974	198918065	E069	12901
chr2	198918578	198918696	E069	13505
chr2	198930117	198930438	E069	25044
chr2	198945273	198945529	E069	40200
chr2	198894809	198894947	E070	-10126
chr2	198896952	198897006	E070	-8067
chr2	198898314	198898364	E070	-6709
chr2	198920560	198920776	E070	15487
chr2	198858638	198858821	E071	-46252
chr2	198860594	198860652	E071	-44421
chr2	198861601	198861700	E071	-43373
chr2	198861897	198861982	E071	-43091
chr2	198862039	198862206	E071	-42867
chr2	198862262	198862312	E071	-42761
chr2	198869003	198869098	E071	-35975
chr2	198869628	198869727	E071	-35346
chr2	198869765	198869846	E071	-35227
chr2	198894292	198894356	E071	-10717
chr2	198894442	198894522	E071	-10551
chr2	198894809	198894947	E071	-10126
chr2	198902752	198902963	E071	-2110
chr2	198903313	198903359	E071	-1714
chr2	198905291	198905433	E071	218
chr2	198905500	198905702	E071	427
chr2	198906774	198907233	E071	1701
chr2	198917564	198917745	E071	12491
chr2	198917974	198918065	E071	12901
chr2	198918578	198918696	E071	13505
chr2	198919150	198919308	E071	14077
chr2	198919509	198919737	E071	14436
chr2	198919820	198920207	E071	14747
chr2	198920560	198920776	E071	15487
chr2	198925168	198925266	E071	20095
chr2	198930117	198930438	E071	25044
chr2	198931481	198931548	E071	26408
chr2	198945273	198945529	E071	40200
chr2	198860594	198860652	E072	-44421
chr2	198861601	198861700	E072	-43373
chr2	198861897	198861982	E072	-43091
chr2	198862039	198862206	E072	-42867
chr2	198862262	198862312	E072	-42761
chr2	198870058	198870605	E072	-34468
chr2	198881929	198882001	E072	-23072
chr2	198895428	198895521	E072	-9552
chr2	198902752	198902963	E072	-2110
chr2	198905291	198905433	E072	218
chr2	198905500	198905702	E072	427
chr2	198914419	198914505	E072	9346
chr2	198917974	198918065	E072	12901
chr2	198918578	198918696	E072	13505
chr2	198919150	198919308	E072	14077
chr2	198919509	198919737	E072	14436
chr2	198919820	198920207	E072	14747
chr2	198920560	198920776	E072	15487
chr2	198922587	198922655	E072	17514
chr2	198925168	198925266	E072	20095
chr2	198945273	198945529	E072	40200
chr2	198860594	198860652	E073	-44421
chr2	198861601	198861700	E073	-43373
chr2	198869628	198869727	E073	-35346
chr2	198869765	198869846	E073	-35227
chr2	198870058	198870605	E073	-34468
chr2	198918578	198918696	E073	13505
chr2	198919150	198919308	E073	14077
chr2	198919509	198919737	E073	14436
chr2	198860594	198860652	E074	-44421
chr2	198861601	198861700	E074	-43373
chr2	198861897	198861982	E074	-43091
chr2	198862039	198862206	E074	-42867
chr2	198862262	198862312	E074	-42761
chr2	198863014	198863054	E074	-42019
chr2	198868844	198868923	E074	-36150
chr2	198869003	198869098	E074	-35975
chr2	198869628	198869727	E074	-35346
chr2	198869765	198869846	E074	-35227
chr2	198881929	198882001	E074	-23072
chr2	198894292	198894356	E074	-10717
chr2	198894442	198894522	E074	-10551
chr2	198894809	198894947	E074	-10126
chr2	198895156	198895261	E074	-9812
chr2	198895311	198895383	E074	-9690
chr2	198902752	198902963	E074	-2110
chr2	198905291	198905433	E074	218
chr2	198905500	198905702	E074	427
chr2	198906774	198907233	E074	1701
chr2	198917564	198917745	E074	12491
chr2	198917974	198918065	E074	12901
chr2	198918578	198918696	E074	13505
chr2	198919150	198919308	E074	14077
chr2	198919509	198919737	E074	14436
chr2	198919820	198920207	E074	14747
chr2	198920560	198920776	E074	15487
chr2	198930117	198930438	E074	25044
chr2	198931481	198931548	E074	26408
chr2	198945273	198945529	E074	40200
chr2	198945273	198945529	E081	40200