rs7587251

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0416 (12448/29912,GnomAD)
G=0417 (12142/29118,TOPMED)
G=0403 (2017/5008,1000G)
T==0480 (1850/3854,ALSPAC)
T==0487 (1806/3708,TWINSUK)

Position: chr2:198065473 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 130 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.198065473T>G
GRCh37.p13 chr 2	NC_000002.11:g.198930197T>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=0.716	G=0.284
1000Genomes	American	Sub	694	T=0.580	G=0.420
1000Genomes	East Asian	Sub	1008	T=0.777	G=0.223
1000Genomes	Europe	Sub	1006	T=0.446	G=0.554
1000Genomes	Global	Study-wide	5008	T=0.597	G=0.403
1000Genomes	South Asian	Sub	978	T=0.420	G=0.580
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.480	G=0.520
The Genome Aggregation Database	African	Sub	8704	T=0.686	G=0.314
The Genome Aggregation Database	American	Sub	838	T=0.660	G=0.340
The Genome Aggregation Database	East Asian	Sub	1614	T=0.804	G=0.196
The Genome Aggregation Database	Europe	Sub	18454	T=0.514	G=0.485
The Genome Aggregation Database	Global	Study-wide	29912	T=0.583	G=0.416
The Genome Aggregation Database	Other	Sub	302	T=0.470	G=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.583	G=0.417
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.487	G=0.513

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
rs7587251	6.06E-06	alcohol consumption	23743675

eQTL of rs7587251 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 rs7587251 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	-34814
chr2	198905291	198905433	E067	-24764
chr2	198918578	198918696	E067	-11501
chr2	198945273	198945529	E067	15076
chr2	198961450	198961502	E067	31253
chr2	198961841	198961912	E067	31644
chr2	198962411	198962470	E067	32214
chr2	198963763	198963935	E067	33566
chr2	198965149	198965308	E067	34952
chr2	198975540	198975603	E067	45343
chr2	198978077	198978371	E067	47880
chr2	198894292	198894356	E068	-35841
chr2	198905291	198905433	E068	-24764
chr2	198905500	198905702	E068	-24495
chr2	198919509	198919737	E068	-10460
chr2	198919820	198920207	E068	-9990
chr2	198920560	198920776	E068	-9421
chr2	198922587	198922655	E068	-7542
chr2	198930117	198930438	E068	0
chr2	198945273	198945529	E068	15076
chr2	198961841	198961912	E068	31644
chr2	198965149	198965308	E068	34952
chr2	198881929	198882001	E069	-48196
chr2	198895156	198895261	E069	-34936
chr2	198895311	198895383	E069	-34814
chr2	198895428	198895521	E069	-34676
chr2	198902752	198902963	E069	-27234
chr2	198905291	198905433	E069	-24764
chr2	198905500	198905702	E069	-24495
chr2	198906774	198907233	E069	-22964
chr2	198917564	198917745	E069	-12452
chr2	198917974	198918065	E069	-12132
chr2	198918578	198918696	E069	-11501
chr2	198930117	198930438	E069	0
chr2	198945273	198945529	E069	15076
chr2	198961841	198961912	E069	31644
chr2	198962411	198962470	E069	32214
chr2	198963763	198963935	E069	33566
chr2	198965149	198965308	E069	34952
chr2	198975540	198975603	E069	45343
chr2	198978425	198978498	E069	48228
chr2	198894809	198894947	E070	-35250
chr2	198896952	198897006	E070	-33191
chr2	198898314	198898364	E070	-31833
chr2	198920560	198920776	E070	-9421
chr2	198894292	198894356	E071	-35841
chr2	198894442	198894522	E071	-35675
chr2	198894809	198894947	E071	-35250
chr2	198902752	198902963	E071	-27234
chr2	198903313	198903359	E071	-26838
chr2	198905291	198905433	E071	-24764
chr2	198905500	198905702	E071	-24495
chr2	198906774	198907233	E071	-22964
chr2	198917564	198917745	E071	-12452
chr2	198917974	198918065	E071	-12132
chr2	198918578	198918696	E071	-11501
chr2	198919150	198919308	E071	-10889
chr2	198919509	198919737	E071	-10460
chr2	198919820	198920207	E071	-9990
chr2	198920560	198920776	E071	-9421
chr2	198925168	198925266	E071	-4931
chr2	198930117	198930438	E071	0
chr2	198931481	198931548	E071	1284
chr2	198945273	198945529	E071	15076
chr2	198960865	198960964	E071	30668
chr2	198961450	198961502	E071	31253
chr2	198961841	198961912	E071	31644
chr2	198962411	198962470	E071	32214
chr2	198963763	198963935	E071	33566
chr2	198965149	198965308	E071	34952
chr2	198975540	198975603	E071	45343
chr2	198977050	198977114	E071	46853
chr2	198881929	198882001	E072	-48196
chr2	198895428	198895521	E072	-34676
chr2	198902752	198902963	E072	-27234
chr2	198905291	198905433	E072	-24764
chr2	198905500	198905702	E072	-24495
chr2	198914419	198914505	E072	-15692
chr2	198917974	198918065	E072	-12132
chr2	198918578	198918696	E072	-11501
chr2	198919150	198919308	E072	-10889
chr2	198919509	198919737	E072	-10460
chr2	198919820	198920207	E072	-9990
chr2	198920560	198920776	E072	-9421
chr2	198922587	198922655	E072	-7542
chr2	198925168	198925266	E072	-4931
chr2	198945273	198945529	E072	15076
chr2	198961841	198961912	E072	31644
chr2	198962411	198962470	E072	32214
chr2	198965149	198965308	E072	34952
chr2	198975540	198975603	E072	45343
chr2	198977050	198977114	E072	46853
chr2	198978077	198978371	E072	47880
chr2	198918578	198918696	E073	-11501
chr2	198919150	198919308	E073	-10889
chr2	198919509	198919737	E073	-10460
chr2	198962411	198962470	E073	32214
chr2	198965149	198965308	E073	34952
chr2	198881929	198882001	E074	-48196
chr2	198894292	198894356	E074	-35841
chr2	198894442	198894522	E074	-35675
chr2	198894809	198894947	E074	-35250
chr2	198895156	198895261	E074	-34936
chr2	198895311	198895383	E074	-34814
chr2	198902752	198902963	E074	-27234
chr2	198905291	198905433	E074	-24764
chr2	198905500	198905702	E074	-24495
chr2	198906774	198907233	E074	-22964
chr2	198917564	198917745	E074	-12452
chr2	198917974	198918065	E074	-12132
chr2	198918578	198918696	E074	-11501
chr2	198919150	198919308	E074	-10889
chr2	198919509	198919737	E074	-10460
chr2	198919820	198920207	E074	-9990
chr2	198920560	198920776	E074	-9421
chr2	198930117	198930438	E074	0
chr2	198931481	198931548	E074	1284
chr2	198945273	198945529	E074	15076
chr2	198961841	198961912	E074	31644
chr2	198962411	198962470	E074	32214
chr2	198963763	198963935	E074	33566
chr2	198965149	198965308	E074	34952
chr2	198975540	198975603	E074	45343
chr2	198978077	198978371	E074	47880
chr2	198978425	198978498	E074	48228
chr2	198978866	198979373	E074	48669
chr2	198979410	198979460	E074	49213
chr2	198979807	198979926	E074	49610
chr2	198980083	198980143	E074	49886
chr2	198945273	198945529	E081	15076