rs1541953

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0399 (11934/29910,GnomAD)
T=0388 (11324/29118,TOPMED)
T=0380 (1905/5008,1000G)
A==0494 (1904/3854,ALSPAC)
T=0497 (1842/3708,TWINSUK)

Position: chr2:198033620 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 140 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.198033620A>T
GRCh37.p13 chr 2	NC_000002.11:g.198898344A>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=0.758	T=0.242
1000Genomes	American	Sub	694	A=0.600	T=0.400
1000Genomes	East Asian	Sub	1008	A=0.780	T=0.220
1000Genomes	Europe	Sub	1006	A=0.454	T=0.546
1000Genomes	Global	Study-wide	5008	A=0.620	T=0.380
1000Genomes	South Asian	Sub	978	A=0.450	T=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.494	T=0.506
The Genome Aggregation Database	African	Sub	8712	A=0.713	T=0.287
The Genome Aggregation Database	American	Sub	838	A=0.670	T=0.330
The Genome Aggregation Database	East Asian	Sub	1606	A=0.801	T=0.199
The Genome Aggregation Database	Europe	Sub	18452	A=0.529	T=0.470
The Genome Aggregation Database	Global	Study-wide	29910	A=0.601	T=0.399
The Genome Aggregation Database	Other	Sub	302	A=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.611	T=0.388
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.503	T=0.497

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
rs1541953	1.06E-05	alcohol consumption	23743675

eQTL of rs1541953 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 rs1541953 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	-48081
chr2	198859584	198859710	E067	-38634
chr2	198860594	198860652	E067	-37692
chr2	198861601	198861700	E067	-36644
chr2	198861897	198861982	E067	-36362
chr2	198862039	198862206	E067	-36138
chr2	198862262	198862312	E067	-36032
chr2	198863014	198863054	E067	-35290
chr2	198895311	198895383	E067	-2961
chr2	198905291	198905433	E067	6947
chr2	198918578	198918696	E067	20234
chr2	198945273	198945529	E067	46929
chr2	198860594	198860652	E068	-37692
chr2	198861601	198861700	E068	-36644
chr2	198861897	198861982	E068	-36362
chr2	198869628	198869727	E068	-28617
chr2	198869765	198869846	E068	-28498
chr2	198894292	198894356	E068	-3988
chr2	198905291	198905433	E068	6947
chr2	198905500	198905702	E068	7156
chr2	198919509	198919737	E068	21165
chr2	198919820	198920207	E068	21476
chr2	198920560	198920776	E068	22216
chr2	198922587	198922655	E068	24243
chr2	198930117	198930438	E068	31773
chr2	198945273	198945529	E068	46929
chr2	198849914	198850263	E069	-48081
chr2	198860594	198860652	E069	-37692
chr2	198861601	198861700	E069	-36644
chr2	198869765	198869846	E069	-28498
chr2	198870058	198870605	E069	-27739
chr2	198881929	198882001	E069	-16343
chr2	198895156	198895261	E069	-3083
chr2	198895311	198895383	E069	-2961
chr2	198895428	198895521	E069	-2823
chr2	198902752	198902963	E069	4408
chr2	198905291	198905433	E069	6947
chr2	198905500	198905702	E069	7156
chr2	198906774	198907233	E069	8430
chr2	198917564	198917745	E069	19220
chr2	198917974	198918065	E069	19630
chr2	198918578	198918696	E069	20234
chr2	198930117	198930438	E069	31773
chr2	198945273	198945529	E069	46929
chr2	198894809	198894947	E070	-3397
chr2	198896952	198897006	E070	-1338
chr2	198898314	198898364	E070	0
chr2	198920560	198920776	E070	22216
chr2	198849914	198850263	E071	-48081
chr2	198858638	198858821	E071	-39523
chr2	198860594	198860652	E071	-37692
chr2	198861601	198861700	E071	-36644
chr2	198861897	198861982	E071	-36362
chr2	198862039	198862206	E071	-36138
chr2	198862262	198862312	E071	-36032
chr2	198869003	198869098	E071	-29246
chr2	198869628	198869727	E071	-28617
chr2	198869765	198869846	E071	-28498
chr2	198894292	198894356	E071	-3988
chr2	198894442	198894522	E071	-3822
chr2	198894809	198894947	E071	-3397
chr2	198902752	198902963	E071	4408
chr2	198903313	198903359	E071	4969
chr2	198905291	198905433	E071	6947
chr2	198905500	198905702	E071	7156
chr2	198906774	198907233	E071	8430
chr2	198917564	198917745	E071	19220
chr2	198917974	198918065	E071	19630
chr2	198918578	198918696	E071	20234
chr2	198919150	198919308	E071	20806
chr2	198919509	198919737	E071	21165
chr2	198919820	198920207	E071	21476
chr2	198920560	198920776	E071	22216
chr2	198925168	198925266	E071	26824
chr2	198930117	198930438	E071	31773
chr2	198931481	198931548	E071	33137
chr2	198945273	198945529	E071	46929
chr2	198849914	198850263	E072	-48081
chr2	198860594	198860652	E072	-37692
chr2	198861601	198861700	E072	-36644
chr2	198861897	198861982	E072	-36362
chr2	198862039	198862206	E072	-36138
chr2	198862262	198862312	E072	-36032
chr2	198870058	198870605	E072	-27739
chr2	198881929	198882001	E072	-16343
chr2	198895428	198895521	E072	-2823
chr2	198902752	198902963	E072	4408
chr2	198905291	198905433	E072	6947
chr2	198905500	198905702	E072	7156
chr2	198914419	198914505	E072	16075
chr2	198917974	198918065	E072	19630
chr2	198918578	198918696	E072	20234
chr2	198919150	198919308	E072	20806
chr2	198919509	198919737	E072	21165
chr2	198919820	198920207	E072	21476
chr2	198920560	198920776	E072	22216
chr2	198922587	198922655	E072	24243
chr2	198925168	198925266	E072	26824
chr2	198945273	198945529	E072	46929
chr2	198860594	198860652	E073	-37692
chr2	198861601	198861700	E073	-36644
chr2	198869628	198869727	E073	-28617
chr2	198869765	198869846	E073	-28498
chr2	198870058	198870605	E073	-27739
chr2	198918578	198918696	E073	20234
chr2	198919150	198919308	E073	20806
chr2	198919509	198919737	E073	21165
chr2	198849914	198850263	E074	-48081
chr2	198860594	198860652	E074	-37692
chr2	198861601	198861700	E074	-36644
chr2	198861897	198861982	E074	-36362
chr2	198862039	198862206	E074	-36138
chr2	198862262	198862312	E074	-36032
chr2	198863014	198863054	E074	-35290
chr2	198868844	198868923	E074	-29421
chr2	198869003	198869098	E074	-29246
chr2	198869628	198869727	E074	-28617
chr2	198869765	198869846	E074	-28498
chr2	198881929	198882001	E074	-16343
chr2	198894292	198894356	E074	-3988
chr2	198894442	198894522	E074	-3822
chr2	198894809	198894947	E074	-3397
chr2	198895156	198895261	E074	-3083
chr2	198895311	198895383	E074	-2961
chr2	198902752	198902963	E074	4408
chr2	198905291	198905433	E074	6947
chr2	198905500	198905702	E074	7156
chr2	198906774	198907233	E074	8430
chr2	198917564	198917745	E074	19220
chr2	198917974	198918065	E074	19630
chr2	198918578	198918696	E074	20234
chr2	198919150	198919308	E074	20806
chr2	198919509	198919737	E074	21165
chr2	198919820	198920207	E074	21476
chr2	198920560	198920776	E074	22216
chr2	198930117	198930438	E074	31773
chr2	198931481	198931548	E074	33137
chr2	198945273	198945529	E074	46929
chr2	198945273	198945529	E081	46929
chr2	198849914	198850263	E082	-48081