rs745899

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0428 (12829/29924,GnomAD)
T=0440 (12829/29118,TOPMED)
T=0418 (2092/5008,1000G)
A==0487 (1876/3854,ALSPAC)
A==0496 (1838/3708,TWINSUK)

Position: chr2:198043316 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 134 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.198043316A>T
GRCh37.p13 chr 2	NC_000002.11:g.198908040A>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	A=0.651	T=0.349
1000Genomes	American	Sub	694	A=0.580	T=0.420
1000Genomes	East Asian	Sub	1008	A=0.779	T=0.221
1000Genomes	Europe	Sub	1006	A=0.449	T=0.551
1000Genomes	Global	Study-wide	5008	A=0.582	T=0.418
1000Genomes	South Asian	Sub	978	A=0.430	T=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.487	T=0.513
The Genome Aggregation Database	African	Sub	8708	A=0.630	T=0.370
The Genome Aggregation Database	American	Sub	836	A=0.660	T=0.340
The Genome Aggregation Database	East Asian	Sub	1618	A=0.802	T=0.198
The Genome Aggregation Database	Europe	Sub	18460	A=0.521	T=0.479
The Genome Aggregation Database	Global	Study-wide	29924	A=0.571	T=0.428
The Genome Aggregation Database	Other	Sub	302	A=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.559	T=0.440
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.496	T=0.504

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
rs745899	4.24E-06	alcohol consumption	23743675

eQTL of rs745899 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 rs745899 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	198859584	198859710	E067	-48330
chr2	198860594	198860652	E067	-47388
chr2	198861601	198861700	E067	-46340
chr2	198861897	198861982	E067	-46058
chr2	198862039	198862206	E067	-45834
chr2	198862262	198862312	E067	-45728
chr2	198863014	198863054	E067	-44986
chr2	198895311	198895383	E067	-12657
chr2	198905291	198905433	E067	-2607
chr2	198918578	198918696	E067	10538
chr2	198945273	198945529	E067	37233
chr2	198860594	198860652	E068	-47388
chr2	198861601	198861700	E068	-46340
chr2	198861897	198861982	E068	-46058
chr2	198869628	198869727	E068	-38313
chr2	198869765	198869846	E068	-38194
chr2	198894292	198894356	E068	-13684
chr2	198905291	198905433	E068	-2607
chr2	198905500	198905702	E068	-2338
chr2	198919509	198919737	E068	11469
chr2	198919820	198920207	E068	11780
chr2	198920560	198920776	E068	12520
chr2	198922587	198922655	E068	14547
chr2	198930117	198930438	E068	22077
chr2	198945273	198945529	E068	37233
chr2	198860594	198860652	E069	-47388
chr2	198861601	198861700	E069	-46340
chr2	198869765	198869846	E069	-38194
chr2	198870058	198870605	E069	-37435
chr2	198881929	198882001	E069	-26039
chr2	198895156	198895261	E069	-12779
chr2	198895311	198895383	E069	-12657
chr2	198895428	198895521	E069	-12519
chr2	198902752	198902963	E069	-5077
chr2	198905291	198905433	E069	-2607
chr2	198905500	198905702	E069	-2338
chr2	198906774	198907233	E069	-807
chr2	198917564	198917745	E069	9524
chr2	198917974	198918065	E069	9934
chr2	198918578	198918696	E069	10538
chr2	198930117	198930438	E069	22077
chr2	198945273	198945529	E069	37233
chr2	198894809	198894947	E070	-13093
chr2	198896952	198897006	E070	-11034
chr2	198898314	198898364	E070	-9676
chr2	198920560	198920776	E070	12520
chr2	198858638	198858821	E071	-49219
chr2	198860594	198860652	E071	-47388
chr2	198861601	198861700	E071	-46340
chr2	198861897	198861982	E071	-46058
chr2	198862039	198862206	E071	-45834
chr2	198862262	198862312	E071	-45728
chr2	198869003	198869098	E071	-38942
chr2	198869628	198869727	E071	-38313
chr2	198869765	198869846	E071	-38194
chr2	198894292	198894356	E071	-13684
chr2	198894442	198894522	E071	-13518
chr2	198894809	198894947	E071	-13093
chr2	198902752	198902963	E071	-5077
chr2	198903313	198903359	E071	-4681
chr2	198905291	198905433	E071	-2607
chr2	198905500	198905702	E071	-2338
chr2	198906774	198907233	E071	-807
chr2	198917564	198917745	E071	9524
chr2	198917974	198918065	E071	9934
chr2	198918578	198918696	E071	10538
chr2	198919150	198919308	E071	11110
chr2	198919509	198919737	E071	11469
chr2	198919820	198920207	E071	11780
chr2	198920560	198920776	E071	12520
chr2	198925168	198925266	E071	17128
chr2	198930117	198930438	E071	22077
chr2	198931481	198931548	E071	23441
chr2	198945273	198945529	E071	37233
chr2	198860594	198860652	E072	-47388
chr2	198861601	198861700	E072	-46340
chr2	198861897	198861982	E072	-46058
chr2	198862039	198862206	E072	-45834
chr2	198862262	198862312	E072	-45728
chr2	198870058	198870605	E072	-37435
chr2	198881929	198882001	E072	-26039
chr2	198895428	198895521	E072	-12519
chr2	198902752	198902963	E072	-5077
chr2	198905291	198905433	E072	-2607
chr2	198905500	198905702	E072	-2338
chr2	198914419	198914505	E072	6379
chr2	198917974	198918065	E072	9934
chr2	198918578	198918696	E072	10538
chr2	198919150	198919308	E072	11110
chr2	198919509	198919737	E072	11469
chr2	198919820	198920207	E072	11780
chr2	198920560	198920776	E072	12520
chr2	198922587	198922655	E072	14547
chr2	198925168	198925266	E072	17128
chr2	198945273	198945529	E072	37233
chr2	198860594	198860652	E073	-47388
chr2	198861601	198861700	E073	-46340
chr2	198869628	198869727	E073	-38313
chr2	198869765	198869846	E073	-38194
chr2	198870058	198870605	E073	-37435
chr2	198918578	198918696	E073	10538
chr2	198919150	198919308	E073	11110
chr2	198919509	198919737	E073	11469
chr2	198860594	198860652	E074	-47388
chr2	198861601	198861700	E074	-46340
chr2	198861897	198861982	E074	-46058
chr2	198862039	198862206	E074	-45834
chr2	198862262	198862312	E074	-45728
chr2	198863014	198863054	E074	-44986
chr2	198868844	198868923	E074	-39117
chr2	198869003	198869098	E074	-38942
chr2	198869628	198869727	E074	-38313
chr2	198869765	198869846	E074	-38194
chr2	198881929	198882001	E074	-26039
chr2	198894292	198894356	E074	-13684
chr2	198894442	198894522	E074	-13518
chr2	198894809	198894947	E074	-13093
chr2	198895156	198895261	E074	-12779
chr2	198895311	198895383	E074	-12657
chr2	198902752	198902963	E074	-5077
chr2	198905291	198905433	E074	-2607
chr2	198905500	198905702	E074	-2338
chr2	198906774	198907233	E074	-807
chr2	198917564	198917745	E074	9524
chr2	198917974	198918065	E074	9934
chr2	198918578	198918696	E074	10538
chr2	198919150	198919308	E074	11110
chr2	198919509	198919737	E074	11469
chr2	198919820	198920207	E074	11780
chr2	198920560	198920776	E074	12520
chr2	198930117	198930438	E074	22077
chr2	198931481	198931548	E074	23441
chr2	198945273	198945529	E074	37233
chr2	198945273	198945529	E081	37233