rs10206714

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0431 (12881/29876,GnomAD)
T=0442 (12871/29118,TOPMED)
T=0420 (2105/5008,1000G)

Position: chr2:198041757 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 129 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.198041757C>A
GRCh38.p7 chr 2	NC_000002.12:g.198041757C>T
GRCh37.p13 chr 2	NC_000002.11:g.198906481C>A
GRCh37.p13 chr 2	NC_000002.11:g.198906481C>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=0.643	T=0.357
1000Genomes	American	Sub	694	C=0.580	T=0.420
1000Genomes	East Asian	Sub	1008	C=0.779	T=0.221
1000Genomes	Europe	Sub	1006	C=0.448	T=0.552
1000Genomes	Global	Study-wide	5008	C=0.580	T=0.420
1000Genomes	South Asian	Sub	978	C=0.430	T=0.570
The Genome Aggregation Database	African	Sub	8708	C=0.621	T=0.379
The Genome Aggregation Database	American	Sub	828	C=0.660	T=0.34,
The Genome Aggregation Database	East Asian	Sub	1610	C=0.803	T=0.197
The Genome Aggregation Database	Europe	Sub	18428	C=0.521	T=0.478
The Genome Aggregation Database	Global	Study-wide	29876	C=0.568	T=0.431
The Genome Aggregation Database	Other	Sub	302	C=0.480	T=0.52,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.558	T=0.442

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
rs10206714	4.5E-06	alcohol consumption	23743675

eQTL of rs10206714 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 rs10206714 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	198895311	198895383	E067	-20351
chr2	198905291	198905433	E067	-10301
chr2	198918578	198918696	E067	2844
chr2	198945273	198945529	E067	29539
chr2	198961450	198961502	E067	45716
chr2	198961841	198961912	E067	46107
chr2	198962411	198962470	E067	46677
chr2	198963763	198963935	E067	48029
chr2	198965149	198965308	E067	49415
chr2	198869628	198869727	E068	-46007
chr2	198869765	198869846	E068	-45888
chr2	198894292	198894356	E068	-21378
chr2	198905291	198905433	E068	-10301
chr2	198905500	198905702	E068	-10032
chr2	198919509	198919737	E068	3775
chr2	198919820	198920207	E068	4086
chr2	198920560	198920776	E068	4826
chr2	198922587	198922655	E068	6853
chr2	198930117	198930438	E068	14383
chr2	198945273	198945529	E068	29539
chr2	198961841	198961912	E068	46107
chr2	198965149	198965308	E068	49415
chr2	198869765	198869846	E069	-45888
chr2	198870058	198870605	E069	-45129
chr2	198881929	198882001	E069	-33733
chr2	198895156	198895261	E069	-20473
chr2	198895311	198895383	E069	-20351
chr2	198895428	198895521	E069	-20213
chr2	198902752	198902963	E069	-12771
chr2	198905291	198905433	E069	-10301
chr2	198905500	198905702	E069	-10032
chr2	198906774	198907233	E069	-8501
chr2	198917564	198917745	E069	1830
chr2	198917974	198918065	E069	2240
chr2	198918578	198918696	E069	2844
chr2	198930117	198930438	E069	14383
chr2	198945273	198945529	E069	29539
chr2	198961841	198961912	E069	46107
chr2	198962411	198962470	E069	46677
chr2	198963763	198963935	E069	48029
chr2	198965149	198965308	E069	49415
chr2	198894809	198894947	E070	-20787
chr2	198896952	198897006	E070	-18728
chr2	198898314	198898364	E070	-17370
chr2	198920560	198920776	E070	4826
chr2	198869003	198869098	E071	-46636
chr2	198869628	198869727	E071	-46007
chr2	198869765	198869846	E071	-45888
chr2	198894292	198894356	E071	-21378
chr2	198894442	198894522	E071	-21212
chr2	198894809	198894947	E071	-20787
chr2	198902752	198902963	E071	-12771
chr2	198903313	198903359	E071	-12375
chr2	198905291	198905433	E071	-10301
chr2	198905500	198905702	E071	-10032
chr2	198906774	198907233	E071	-8501
chr2	198917564	198917745	E071	1830
chr2	198917974	198918065	E071	2240
chr2	198918578	198918696	E071	2844
chr2	198919150	198919308	E071	3416
chr2	198919509	198919737	E071	3775
chr2	198919820	198920207	E071	4086
chr2	198920560	198920776	E071	4826
chr2	198925168	198925266	E071	9434
chr2	198930117	198930438	E071	14383
chr2	198931481	198931548	E071	15747
chr2	198945273	198945529	E071	29539
chr2	198960865	198960964	E071	45131
chr2	198961450	198961502	E071	45716
chr2	198961841	198961912	E071	46107
chr2	198962411	198962470	E071	46677
chr2	198963763	198963935	E071	48029
chr2	198965149	198965308	E071	49415
chr2	198870058	198870605	E072	-45129
chr2	198881929	198882001	E072	-33733
chr2	198895428	198895521	E072	-20213
chr2	198902752	198902963	E072	-12771
chr2	198905291	198905433	E072	-10301
chr2	198905500	198905702	E072	-10032
chr2	198914419	198914505	E072	-1229
chr2	198917974	198918065	E072	2240
chr2	198918578	198918696	E072	2844
chr2	198919150	198919308	E072	3416
chr2	198919509	198919737	E072	3775
chr2	198919820	198920207	E072	4086
chr2	198920560	198920776	E072	4826
chr2	198922587	198922655	E072	6853
chr2	198925168	198925266	E072	9434
chr2	198945273	198945529	E072	29539
chr2	198961841	198961912	E072	46107
chr2	198962411	198962470	E072	46677
chr2	198965149	198965308	E072	49415
chr2	198869628	198869727	E073	-46007
chr2	198869765	198869846	E073	-45888
chr2	198870058	198870605	E073	-45129
chr2	198918578	198918696	E073	2844
chr2	198919150	198919308	E073	3416
chr2	198919509	198919737	E073	3775
chr2	198962411	198962470	E073	46677
chr2	198965149	198965308	E073	49415
chr2	198868844	198868923	E074	-46811
chr2	198869003	198869098	E074	-46636
chr2	198869628	198869727	E074	-46007
chr2	198869765	198869846	E074	-45888
chr2	198881929	198882001	E074	-33733
chr2	198894292	198894356	E074	-21378
chr2	198894442	198894522	E074	-21212
chr2	198894809	198894947	E074	-20787
chr2	198895156	198895261	E074	-20473
chr2	198895311	198895383	E074	-20351
chr2	198902752	198902963	E074	-12771
chr2	198905291	198905433	E074	-10301
chr2	198905500	198905702	E074	-10032
chr2	198906774	198907233	E074	-8501
chr2	198917564	198917745	E074	1830
chr2	198917974	198918065	E074	2240
chr2	198918578	198918696	E074	2844
chr2	198919150	198919308	E074	3416
chr2	198919509	198919737	E074	3775
chr2	198919820	198920207	E074	4086
chr2	198920560	198920776	E074	4826
chr2	198930117	198930438	E074	14383
chr2	198931481	198931548	E074	15747
chr2	198945273	198945529	E074	29539
chr2	198961841	198961912	E074	46107
chr2	198962411	198962470	E074	46677
chr2	198963763	198963935	E074	48029
chr2	198965149	198965308	E074	49415
chr2	198945273	198945529	E081	29539