rs10497813

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0412 (12337/29912,GnomAD)
T=0414 (12078/29118,TOPMED)
T=0401 (2010/5008,1000G)
G==0489 (1884/3854,ALSPAC)
G==0497 (1842/3708,TWINSUK)

Position: chr2:198049348 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 122 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.198049348G>T
GRCh37.p13 chr 2	NC_000002.11:g.198914072G>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	G=0.710	T=0.290
1000Genomes	American	Sub	694	G=0.590	T=0.410
1000Genomes	East Asian	Sub	1008	G=0.778	T=0.222
1000Genomes	Europe	Sub	1006	G=0.449	T=0.551
1000Genomes	Global	Study-wide	5008	G=0.599	T=0.401
1000Genomes	South Asian	Sub	978	G=0.430	T=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.489	T=0.511
The Genome Aggregation Database	African	Sub	8706	G=0.682	T=0.318
The Genome Aggregation Database	American	Sub	834	G=0.670	T=0.330
The Genome Aggregation Database	East Asian	Sub	1616	G=0.804	T=0.196
The Genome Aggregation Database	Europe	Sub	18456	G=0.522	T=0.477
The Genome Aggregation Database	Global	Study-wide	29912	G=0.587	T=0.412
The Genome Aggregation Database	Other	Sub	300	G=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.585	T=0.414
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.497	T=0.503

PMID	Title	Author	Journal
23817569	A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.	Hinds DA	Nat Genet
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
rs10497813	4.36E-06	alcohol consumption	23743675

eQTL of rs10497813 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 rs10497813 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	-18689
chr2	198905291	198905433	E067	-8639
chr2	198918578	198918696	E067	4506
chr2	198945273	198945529	E067	31201
chr2	198961450	198961502	E067	47378
chr2	198961841	198961912	E067	47769
chr2	198962411	198962470	E067	48339
chr2	198963763	198963935	E067	49691
chr2	198869628	198869727	E068	-44345
chr2	198869765	198869846	E068	-44226
chr2	198894292	198894356	E068	-19716
chr2	198905291	198905433	E068	-8639
chr2	198905500	198905702	E068	-8370
chr2	198919509	198919737	E068	5437
chr2	198919820	198920207	E068	5748
chr2	198920560	198920776	E068	6488
chr2	198922587	198922655	E068	8515
chr2	198930117	198930438	E068	16045
chr2	198945273	198945529	E068	31201
chr2	198961841	198961912	E068	47769
chr2	198869765	198869846	E069	-44226
chr2	198870058	198870605	E069	-43467
chr2	198881929	198882001	E069	-32071
chr2	198895156	198895261	E069	-18811
chr2	198895311	198895383	E069	-18689
chr2	198895428	198895521	E069	-18551
chr2	198902752	198902963	E069	-11109
chr2	198905291	198905433	E069	-8639
chr2	198905500	198905702	E069	-8370
chr2	198906774	198907233	E069	-6839
chr2	198917564	198917745	E069	3492
chr2	198917974	198918065	E069	3902
chr2	198918578	198918696	E069	4506
chr2	198930117	198930438	E069	16045
chr2	198945273	198945529	E069	31201
chr2	198961841	198961912	E069	47769
chr2	198962411	198962470	E069	48339
chr2	198963763	198963935	E069	49691
chr2	198894809	198894947	E070	-19125
chr2	198896952	198897006	E070	-17066
chr2	198898314	198898364	E070	-15708
chr2	198920560	198920776	E070	6488
chr2	198869003	198869098	E071	-44974
chr2	198869628	198869727	E071	-44345
chr2	198869765	198869846	E071	-44226
chr2	198894292	198894356	E071	-19716
chr2	198894442	198894522	E071	-19550
chr2	198894809	198894947	E071	-19125
chr2	198902752	198902963	E071	-11109
chr2	198903313	198903359	E071	-10713
chr2	198905291	198905433	E071	-8639
chr2	198905500	198905702	E071	-8370
chr2	198906774	198907233	E071	-6839
chr2	198917564	198917745	E071	3492
chr2	198917974	198918065	E071	3902
chr2	198918578	198918696	E071	4506
chr2	198919150	198919308	E071	5078
chr2	198919509	198919737	E071	5437
chr2	198919820	198920207	E071	5748
chr2	198920560	198920776	E071	6488
chr2	198925168	198925266	E071	11096
chr2	198930117	198930438	E071	16045
chr2	198931481	198931548	E071	17409
chr2	198945273	198945529	E071	31201
chr2	198960865	198960964	E071	46793
chr2	198961450	198961502	E071	47378
chr2	198961841	198961912	E071	47769
chr2	198962411	198962470	E071	48339
chr2	198963763	198963935	E071	49691
chr2	198870058	198870605	E072	-43467
chr2	198881929	198882001	E072	-32071
chr2	198895428	198895521	E072	-18551
chr2	198902752	198902963	E072	-11109
chr2	198905291	198905433	E072	-8639
chr2	198905500	198905702	E072	-8370
chr2	198914419	198914505	E072	347
chr2	198917974	198918065	E072	3902
chr2	198918578	198918696	E072	4506
chr2	198919150	198919308	E072	5078
chr2	198919509	198919737	E072	5437
chr2	198919820	198920207	E072	5748
chr2	198920560	198920776	E072	6488
chr2	198922587	198922655	E072	8515
chr2	198925168	198925266	E072	11096
chr2	198945273	198945529	E072	31201
chr2	198961841	198961912	E072	47769
chr2	198962411	198962470	E072	48339
chr2	198869628	198869727	E073	-44345
chr2	198869765	198869846	E073	-44226
chr2	198870058	198870605	E073	-43467
chr2	198918578	198918696	E073	4506
chr2	198919150	198919308	E073	5078
chr2	198919509	198919737	E073	5437
chr2	198962411	198962470	E073	48339
chr2	198868844	198868923	E074	-45149
chr2	198869003	198869098	E074	-44974
chr2	198869628	198869727	E074	-44345
chr2	198869765	198869846	E074	-44226
chr2	198881929	198882001	E074	-32071
chr2	198894292	198894356	E074	-19716
chr2	198894442	198894522	E074	-19550
chr2	198894809	198894947	E074	-19125
chr2	198895156	198895261	E074	-18811
chr2	198895311	198895383	E074	-18689
chr2	198902752	198902963	E074	-11109
chr2	198905291	198905433	E074	-8639
chr2	198905500	198905702	E074	-8370
chr2	198906774	198907233	E074	-6839
chr2	198917564	198917745	E074	3492
chr2	198917974	198918065	E074	3902
chr2	198918578	198918696	E074	4506
chr2	198919150	198919308	E074	5078
chr2	198919509	198919737	E074	5437
chr2	198919820	198920207	E074	5748
chr2	198920560	198920776	E074	6488
chr2	198930117	198930438	E074	16045
chr2	198931481	198931548	E074	17409
chr2	198945273	198945529	E074	31201
chr2	198961841	198961912	E074	47769
chr2	198962411	198962470	E074	48339
chr2	198963763	198963935	E074	49691
chr2	198945273	198945529	E081	31201