rs2196172

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0461 (13799/29896,GnomAD)
G=0488 (14212/29118,TOPMED)
G=0449 (2249/5008,1000G)
T==0490 (1889/3854,ALSPAC)
T==0498 (1845/3708,TWINSUK)

Position: chr2:198025169 (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.198025169T>G
GRCh37.p13 chr 2	NC_000002.11:g.198889893T>G

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=0.508	G=0.492
1000Genomes	American	Sub	694	T=0.580	G=0.420
1000Genomes	East Asian	Sub	1008	T=0.780	G=0.220
1000Genomes	Europe	Sub	1006	T=0.454	G=0.546
1000Genomes	Global	Study-wide	5008	T=0.551	G=0.449
1000Genomes	South Asian	Sub	978	T=0.450	G=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.490	G=0.510
The Genome Aggregation Database	African	Sub	8708	T=0.499	G=0.501
The Genome Aggregation Database	American	Sub	838	T=0.660	G=0.340
The Genome Aggregation Database	East Asian	Sub	1616	T=0.801	G=0.199
The Genome Aggregation Database	Europe	Sub	18432	T=0.529	G=0.470
The Genome Aggregation Database	Global	Study-wide	29896	T=0.538	G=0.461
The Genome Aggregation Database	Other	Sub	302	T=0.480	G=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.511	G=0.488
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.498	G=0.502

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
rs2196172	2.17E-05	alcohol consumption	23743675

eQTL of rs2196172 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:198889893	SF3B1	ENSG00000115524.11	T>G	7.6222e-4	590078	Caudate_basal_ganglia

meQTL of rs2196172 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	-39630
chr2	198859584	198859710	E067	-30183
chr2	198860594	198860652	E067	-29241
chr2	198861601	198861700	E067	-28193
chr2	198861897	198861982	E067	-27911
chr2	198862039	198862206	E067	-27687
chr2	198862262	198862312	E067	-27581
chr2	198863014	198863054	E067	-26839
chr2	198895311	198895383	E067	5418
chr2	198905291	198905433	E067	15398
chr2	198918578	198918696	E067	28685
chr2	198860594	198860652	E068	-29241
chr2	198861601	198861700	E068	-28193
chr2	198861897	198861982	E068	-27911
chr2	198869628	198869727	E068	-20166
chr2	198869765	198869846	E068	-20047
chr2	198894292	198894356	E068	4399
chr2	198905291	198905433	E068	15398
chr2	198905500	198905702	E068	15607
chr2	198919509	198919737	E068	29616
chr2	198919820	198920207	E068	29927
chr2	198920560	198920776	E068	30667
chr2	198922587	198922655	E068	32694
chr2	198930117	198930438	E068	40224
chr2	198849914	198850263	E069	-39630
chr2	198860594	198860652	E069	-29241
chr2	198861601	198861700	E069	-28193
chr2	198869765	198869846	E069	-20047
chr2	198870058	198870605	E069	-19288
chr2	198881929	198882001	E069	-7892
chr2	198895156	198895261	E069	5263
chr2	198895311	198895383	E069	5418
chr2	198895428	198895521	E069	5535
chr2	198902752	198902963	E069	12859
chr2	198905291	198905433	E069	15398
chr2	198905500	198905702	E069	15607
chr2	198906774	198907233	E069	16881
chr2	198917564	198917745	E069	27671
chr2	198917974	198918065	E069	28081
chr2	198918578	198918696	E069	28685
chr2	198930117	198930438	E069	40224
chr2	198894809	198894947	E070	4916
chr2	198896952	198897006	E070	7059
chr2	198898314	198898364	E070	8421
chr2	198920560	198920776	E070	30667
chr2	198849914	198850263	E071	-39630
chr2	198858638	198858821	E071	-31072
chr2	198860594	198860652	E071	-29241
chr2	198861601	198861700	E071	-28193
chr2	198861897	198861982	E071	-27911
chr2	198862039	198862206	E071	-27687
chr2	198862262	198862312	E071	-27581
chr2	198869003	198869098	E071	-20795
chr2	198869628	198869727	E071	-20166
chr2	198869765	198869846	E071	-20047
chr2	198894292	198894356	E071	4399
chr2	198894442	198894522	E071	4549
chr2	198894809	198894947	E071	4916
chr2	198902752	198902963	E071	12859
chr2	198903313	198903359	E071	13420
chr2	198905291	198905433	E071	15398
chr2	198905500	198905702	E071	15607
chr2	198906774	198907233	E071	16881
chr2	198917564	198917745	E071	27671
chr2	198917974	198918065	E071	28081
chr2	198918578	198918696	E071	28685
chr2	198919150	198919308	E071	29257
chr2	198919509	198919737	E071	29616
chr2	198919820	198920207	E071	29927
chr2	198920560	198920776	E071	30667
chr2	198925168	198925266	E071	35275
chr2	198930117	198930438	E071	40224
chr2	198931481	198931548	E071	41588
chr2	198849914	198850263	E072	-39630
chr2	198860594	198860652	E072	-29241
chr2	198861601	198861700	E072	-28193
chr2	198861897	198861982	E072	-27911
chr2	198862039	198862206	E072	-27687
chr2	198862262	198862312	E072	-27581
chr2	198870058	198870605	E072	-19288
chr2	198881929	198882001	E072	-7892
chr2	198895428	198895521	E072	5535
chr2	198902752	198902963	E072	12859
chr2	198905291	198905433	E072	15398
chr2	198905500	198905702	E072	15607
chr2	198914419	198914505	E072	24526
chr2	198917974	198918065	E072	28081
chr2	198918578	198918696	E072	28685
chr2	198919150	198919308	E072	29257
chr2	198919509	198919737	E072	29616
chr2	198919820	198920207	E072	29927
chr2	198920560	198920776	E072	30667
chr2	198922587	198922655	E072	32694
chr2	198925168	198925266	E072	35275
chr2	198860594	198860652	E073	-29241
chr2	198861601	198861700	E073	-28193
chr2	198869628	198869727	E073	-20166
chr2	198869765	198869846	E073	-20047
chr2	198870058	198870605	E073	-19288
chr2	198918578	198918696	E073	28685
chr2	198919150	198919308	E073	29257
chr2	198919509	198919737	E073	29616
chr2	198849914	198850263	E074	-39630
chr2	198860594	198860652	E074	-29241
chr2	198861601	198861700	E074	-28193
chr2	198861897	198861982	E074	-27911
chr2	198862039	198862206	E074	-27687
chr2	198862262	198862312	E074	-27581
chr2	198863014	198863054	E074	-26839
chr2	198868844	198868923	E074	-20970
chr2	198869003	198869098	E074	-20795
chr2	198869628	198869727	E074	-20166
chr2	198869765	198869846	E074	-20047
chr2	198881929	198882001	E074	-7892
chr2	198894292	198894356	E074	4399
chr2	198894442	198894522	E074	4549
chr2	198894809	198894947	E074	4916
chr2	198895156	198895261	E074	5263
chr2	198895311	198895383	E074	5418
chr2	198902752	198902963	E074	12859
chr2	198905291	198905433	E074	15398
chr2	198905500	198905702	E074	15607
chr2	198906774	198907233	E074	16881
chr2	198917564	198917745	E074	27671
chr2	198917974	198918065	E074	28081
chr2	198918578	198918696	E074	28685
chr2	198919150	198919308	E074	29257
chr2	198919509	198919737	E074	29616
chr2	198919820	198920207	E074	29927
chr2	198920560	198920776	E074	30667
chr2	198930117	198930438	E074	40224
chr2	198931481	198931548	E074	41588
chr2	198849914	198850263	E082	-39630