rs10184227

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0462 (13778/29818,GnomAD)
T=0490 (14282/29118,TOPMED)
T=0450 (2254/5008,1000G)
C==0494 (1902/3854,ALSPAC)
T=0496 (1840/3708,TWINSUK)

Position: chr2:198029581 (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.198029581C>T
GRCh37.p13 chr 2	NC_000002.11:g.198894305C>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=0.504	T=0.496
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	8684	C=0.494	T=0.506
The Genome Aggregation Database	American	Sub	832	C=0.660	T=0.340
The Genome Aggregation Database	East Asian	Sub	1598	C=0.805	T=0.195
The Genome Aggregation Database	Europe	Sub	18402	C=0.530	T=0.469
The Genome Aggregation Database	Global	Study-wide	29818	C=0.537	T=0.462
The Genome Aggregation Database	Other	Sub	302	C=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.509	T=0.490
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
rs10184227	1.11E-05	alcohol consumption	23743675

eQTL of rs10184227 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:198894305	SF3B1	ENSG00000115524.11	C>T	7.6222e-4	594490	Caudate_basal_ganglia

meQTL of rs10184227 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	-44042
chr2	198859584	198859710	E067	-34595
chr2	198860594	198860652	E067	-33653
chr2	198861601	198861700	E067	-32605
chr2	198861897	198861982	E067	-32323
chr2	198862039	198862206	E067	-32099
chr2	198862262	198862312	E067	-31993
chr2	198863014	198863054	E067	-31251
chr2	198895311	198895383	E067	1006
chr2	198905291	198905433	E067	10986
chr2	198918578	198918696	E067	24273
chr2	198860594	198860652	E068	-33653
chr2	198861601	198861700	E068	-32605
chr2	198861897	198861982	E068	-32323
chr2	198869628	198869727	E068	-24578
chr2	198869765	198869846	E068	-24459
chr2	198894292	198894356	E068	0
chr2	198905291	198905433	E068	10986
chr2	198905500	198905702	E068	11195
chr2	198919509	198919737	E068	25204
chr2	198919820	198920207	E068	25515
chr2	198920560	198920776	E068	26255
chr2	198922587	198922655	E068	28282
chr2	198930117	198930438	E068	35812
chr2	198849914	198850263	E069	-44042
chr2	198860594	198860652	E069	-33653
chr2	198861601	198861700	E069	-32605
chr2	198869765	198869846	E069	-24459
chr2	198870058	198870605	E069	-23700
chr2	198881929	198882001	E069	-12304
chr2	198895156	198895261	E069	851
chr2	198895311	198895383	E069	1006
chr2	198895428	198895521	E069	1123
chr2	198902752	198902963	E069	8447
chr2	198905291	198905433	E069	10986
chr2	198905500	198905702	E069	11195
chr2	198906774	198907233	E069	12469
chr2	198917564	198917745	E069	23259
chr2	198917974	198918065	E069	23669
chr2	198918578	198918696	E069	24273
chr2	198930117	198930438	E069	35812
chr2	198894809	198894947	E070	504
chr2	198896952	198897006	E070	2647
chr2	198898314	198898364	E070	4009
chr2	198920560	198920776	E070	26255
chr2	198849914	198850263	E071	-44042
chr2	198858638	198858821	E071	-35484
chr2	198860594	198860652	E071	-33653
chr2	198861601	198861700	E071	-32605
chr2	198861897	198861982	E071	-32323
chr2	198862039	198862206	E071	-32099
chr2	198862262	198862312	E071	-31993
chr2	198869003	198869098	E071	-25207
chr2	198869628	198869727	E071	-24578
chr2	198869765	198869846	E071	-24459
chr2	198894292	198894356	E071	0
chr2	198894442	198894522	E071	137
chr2	198894809	198894947	E071	504
chr2	198902752	198902963	E071	8447
chr2	198903313	198903359	E071	9008
chr2	198905291	198905433	E071	10986
chr2	198905500	198905702	E071	11195
chr2	198906774	198907233	E071	12469
chr2	198917564	198917745	E071	23259
chr2	198917974	198918065	E071	23669
chr2	198918578	198918696	E071	24273
chr2	198919150	198919308	E071	24845
chr2	198919509	198919737	E071	25204
chr2	198919820	198920207	E071	25515
chr2	198920560	198920776	E071	26255
chr2	198925168	198925266	E071	30863
chr2	198930117	198930438	E071	35812
chr2	198931481	198931548	E071	37176
chr2	198849914	198850263	E072	-44042
chr2	198860594	198860652	E072	-33653
chr2	198861601	198861700	E072	-32605
chr2	198861897	198861982	E072	-32323
chr2	198862039	198862206	E072	-32099
chr2	198862262	198862312	E072	-31993
chr2	198870058	198870605	E072	-23700
chr2	198881929	198882001	E072	-12304
chr2	198895428	198895521	E072	1123
chr2	198902752	198902963	E072	8447
chr2	198905291	198905433	E072	10986
chr2	198905500	198905702	E072	11195
chr2	198914419	198914505	E072	20114
chr2	198917974	198918065	E072	23669
chr2	198918578	198918696	E072	24273
chr2	198919150	198919308	E072	24845
chr2	198919509	198919737	E072	25204
chr2	198919820	198920207	E072	25515
chr2	198920560	198920776	E072	26255
chr2	198922587	198922655	E072	28282
chr2	198925168	198925266	E072	30863
chr2	198860594	198860652	E073	-33653
chr2	198861601	198861700	E073	-32605
chr2	198869628	198869727	E073	-24578
chr2	198869765	198869846	E073	-24459
chr2	198870058	198870605	E073	-23700
chr2	198918578	198918696	E073	24273
chr2	198919150	198919308	E073	24845
chr2	198919509	198919737	E073	25204
chr2	198849914	198850263	E074	-44042
chr2	198860594	198860652	E074	-33653
chr2	198861601	198861700	E074	-32605
chr2	198861897	198861982	E074	-32323
chr2	198862039	198862206	E074	-32099
chr2	198862262	198862312	E074	-31993
chr2	198863014	198863054	E074	-31251
chr2	198868844	198868923	E074	-25382
chr2	198869003	198869098	E074	-25207
chr2	198869628	198869727	E074	-24578
chr2	198869765	198869846	E074	-24459
chr2	198881929	198882001	E074	-12304
chr2	198894292	198894356	E074	0
chr2	198894442	198894522	E074	137
chr2	198894809	198894947	E074	504
chr2	198895156	198895261	E074	851
chr2	198895311	198895383	E074	1006
chr2	198902752	198902963	E074	8447
chr2	198905291	198905433	E074	10986
chr2	198905500	198905702	E074	11195
chr2	198906774	198907233	E074	12469
chr2	198917564	198917745	E074	23259
chr2	198917974	198918065	E074	23669
chr2	198918578	198918696	E074	24273
chr2	198919150	198919308	E074	24845
chr2	198919509	198919737	E074	25204
chr2	198919820	198920207	E074	25515
chr2	198920560	198920776	E074	26255
chr2	198930117	198930438	E074	35812
chr2	198931481	198931548	E074	37176
chr2	198849914	198850263	E082	-44042