rs11681663

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0463 (13840/29874,GnomAD)
A=0490 (14281/29118,TOPMED)
A=0450 (2253/5008,1000G)
G==0494 (1902/3854,ALSPAC)
A=0498 (1845/3708,TWINSUK)

Position: chr2:198018228 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 144 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.198018228G>A
GRCh37.p13 chr 2	NC_000002.11:g.198882952G>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	G=0.505	A=0.495
1000Genomes	American	Sub	694	G=0.580	A=0.420
1000Genomes	East Asian	Sub	1008	G=0.780	A=0.220
1000Genomes	Europe	Sub	1006	G=0.454	A=0.546
1000Genomes	Global	Study-wide	5008	G=0.550	A=0.450
1000Genomes	South Asian	Sub	978	G=0.450	A=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.494	A=0.506
The Genome Aggregation Database	African	Sub	8696	G=0.493	A=0.507
The Genome Aggregation Database	American	Sub	838	G=0.660	A=0.340
The Genome Aggregation Database	East Asian	Sub	1610	G=0.801	A=0.199
The Genome Aggregation Database	Europe	Sub	18428	G=0.529	A=0.470
The Genome Aggregation Database	Global	Study-wide	29874	G=0.536	A=0.463
The Genome Aggregation Database	Other	Sub	302	G=0.480	A=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.509	A=0.490
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.502	A=0.498

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
rs11681663	1.09E-05	alcohol consumption	23743675

eQTL of rs11681663 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:198882952	SF3B1	ENSG00000115524.11	G>A	7.6222e-4	583137	Caudate_basal_ganglia

meQTL of rs11681663 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	198833824	198833897	E067	-49055
chr2	198837363	198837407	E067	-45545
chr2	198849914	198850263	E067	-32689
chr2	198859584	198859710	E067	-23242
chr2	198860594	198860652	E067	-22300
chr2	198861601	198861700	E067	-21252
chr2	198861897	198861982	E067	-20970
chr2	198862039	198862206	E067	-20746
chr2	198862262	198862312	E067	-20640
chr2	198863014	198863054	E067	-19898
chr2	198895311	198895383	E067	12359
chr2	198905291	198905433	E067	22339
chr2	198918578	198918696	E067	35626
chr2	198860594	198860652	E068	-22300
chr2	198861601	198861700	E068	-21252
chr2	198861897	198861982	E068	-20970
chr2	198869628	198869727	E068	-13225
chr2	198869765	198869846	E068	-13106
chr2	198894292	198894356	E068	11340
chr2	198905291	198905433	E068	22339
chr2	198905500	198905702	E068	22548
chr2	198919509	198919737	E068	36557
chr2	198919820	198920207	E068	36868
chr2	198920560	198920776	E068	37608
chr2	198922587	198922655	E068	39635
chr2	198930117	198930438	E068	47165
chr2	198836717	198837189	E069	-45763
chr2	198837363	198837407	E069	-45545
chr2	198849914	198850263	E069	-32689
chr2	198860594	198860652	E069	-22300
chr2	198861601	198861700	E069	-21252
chr2	198869765	198869846	E069	-13106
chr2	198870058	198870605	E069	-12347
chr2	198881929	198882001	E069	-951
chr2	198895156	198895261	E069	12204
chr2	198895311	198895383	E069	12359
chr2	198895428	198895521	E069	12476
chr2	198902752	198902963	E069	19800
chr2	198905291	198905433	E069	22339
chr2	198905500	198905702	E069	22548
chr2	198906774	198907233	E069	23822
chr2	198917564	198917745	E069	34612
chr2	198917974	198918065	E069	35022
chr2	198918578	198918696	E069	35626
chr2	198930117	198930438	E069	47165
chr2	198894809	198894947	E070	11857
chr2	198896952	198897006	E070	14000
chr2	198898314	198898364	E070	15362
chr2	198920560	198920776	E070	37608
chr2	198836417	198836461	E071	-46491
chr2	198836717	198837189	E071	-45763
chr2	198837363	198837407	E071	-45545
chr2	198838668	198838761	E071	-44191
chr2	198849914	198850263	E071	-32689
chr2	198858638	198858821	E071	-24131
chr2	198860594	198860652	E071	-22300
chr2	198861601	198861700	E071	-21252
chr2	198861897	198861982	E071	-20970
chr2	198862039	198862206	E071	-20746
chr2	198862262	198862312	E071	-20640
chr2	198869003	198869098	E071	-13854
chr2	198869628	198869727	E071	-13225
chr2	198869765	198869846	E071	-13106
chr2	198894292	198894356	E071	11340
chr2	198894442	198894522	E071	11490
chr2	198894809	198894947	E071	11857
chr2	198902752	198902963	E071	19800
chr2	198903313	198903359	E071	20361
chr2	198905291	198905433	E071	22339
chr2	198905500	198905702	E071	22548
chr2	198906774	198907233	E071	23822
chr2	198917564	198917745	E071	34612
chr2	198917974	198918065	E071	35022
chr2	198918578	198918696	E071	35626
chr2	198919150	198919308	E071	36198
chr2	198919509	198919737	E071	36557
chr2	198919820	198920207	E071	36868
chr2	198920560	198920776	E071	37608
chr2	198925168	198925266	E071	42216
chr2	198930117	198930438	E071	47165
chr2	198931481	198931548	E071	48529
chr2	198836717	198837189	E072	-45763
chr2	198837363	198837407	E072	-45545
chr2	198838668	198838761	E072	-44191
chr2	198849914	198850263	E072	-32689
chr2	198860594	198860652	E072	-22300
chr2	198861601	198861700	E072	-21252
chr2	198861897	198861982	E072	-20970
chr2	198862039	198862206	E072	-20746
chr2	198862262	198862312	E072	-20640
chr2	198870058	198870605	E072	-12347
chr2	198881929	198882001	E072	-951
chr2	198895428	198895521	E072	12476
chr2	198902752	198902963	E072	19800
chr2	198905291	198905433	E072	22339
chr2	198905500	198905702	E072	22548
chr2	198914419	198914505	E072	31467
chr2	198917974	198918065	E072	35022
chr2	198918578	198918696	E072	35626
chr2	198919150	198919308	E072	36198
chr2	198919509	198919737	E072	36557
chr2	198919820	198920207	E072	36868
chr2	198920560	198920776	E072	37608
chr2	198922587	198922655	E072	39635
chr2	198925168	198925266	E072	42216
chr2	198860594	198860652	E073	-22300
chr2	198861601	198861700	E073	-21252
chr2	198869628	198869727	E073	-13225
chr2	198869765	198869846	E073	-13106
chr2	198870058	198870605	E073	-12347
chr2	198918578	198918696	E073	35626
chr2	198919150	198919308	E073	36198
chr2	198919509	198919737	E073	36557
chr2	198849914	198850263	E074	-32689
chr2	198860594	198860652	E074	-22300
chr2	198861601	198861700	E074	-21252
chr2	198861897	198861982	E074	-20970
chr2	198862039	198862206	E074	-20746
chr2	198862262	198862312	E074	-20640
chr2	198863014	198863054	E074	-19898
chr2	198868844	198868923	E074	-14029
chr2	198869003	198869098	E074	-13854
chr2	198869628	198869727	E074	-13225
chr2	198869765	198869846	E074	-13106
chr2	198881929	198882001	E074	-951
chr2	198894292	198894356	E074	11340
chr2	198894442	198894522	E074	11490
chr2	198894809	198894947	E074	11857
chr2	198895156	198895261	E074	12204
chr2	198895311	198895383	E074	12359
chr2	198902752	198902963	E074	19800
chr2	198905291	198905433	E074	22339
chr2	198905500	198905702	E074	22548
chr2	198906774	198907233	E074	23822
chr2	198917564	198917745	E074	34612
chr2	198917974	198918065	E074	35022
chr2	198918578	198918696	E074	35626
chr2	198919150	198919308	E074	36198
chr2	198919509	198919737	E074	36557
chr2	198919820	198920207	E074	36868
chr2	198920560	198920776	E074	37608
chr2	198930117	198930438	E074	47165
chr2	198931481	198931548	E074	48529
chr2	198849914	198850263	E082	-32689