rs1025549

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0461 (13810/29902,GnomAD)
A=0488 (14212/29118,TOPMED)
A=0449 (2249/5008,1000G)
G==0494 (1903/3854,ALSPAC)
A=0497 (1843/3708,TWINSUK)

Position: chr2:198016459 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 142 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.198016459G>A
GRCh37.p13 chr 2	NC_000002.11:g.198881183G>A

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=0.509	A=0.491
1000Genomes	American	Sub	694	G=0.580	A=0.420
1000Genomes	East Asian	Sub	1008	G=0.779	A=0.221
1000Genomes	Europe	Sub	1006	G=0.454	A=0.546
1000Genomes	Global	Study-wide	5008	G=0.551	A=0.449
1000Genomes	South Asian	Sub	978	G=0.450	A=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.494	A=0.506
The Genome Aggregation Database	African	Sub	8700	G=0.499	A=0.501
The Genome Aggregation Database	American	Sub	832	G=0.660	A=0.340
The Genome Aggregation Database	East Asian	Sub	1612	G=0.802	A=0.198
The Genome Aggregation Database	Europe	Sub	18456	G=0.529	A=0.471
The Genome Aggregation Database	Global	Study-wide	29902	G=0.538	A=0.461
The Genome Aggregation Database	Other	Sub	302	G=0.480	A=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.511	A=0.488
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.503	A=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
rs1025549	1.05E-05	alcohol consumption	23743675

eQTL of rs1025549 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:198881183	SF3B1	ENSG00000115524.11	G>A	7.6222e-4	581368	Caudate_basal_ganglia

meQTL of rs1025549 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	198833824	198833897	E067	-47286
chr2	198837363	198837407	E067	-43776
chr2	198849914	198850263	E067	-30920
chr2	198859584	198859710	E067	-21473
chr2	198860594	198860652	E067	-20531
chr2	198861601	198861700	E067	-19483
chr2	198861897	198861982	E067	-19201
chr2	198862039	198862206	E067	-18977
chr2	198862262	198862312	E067	-18871
chr2	198863014	198863054	E067	-18129
chr2	198895311	198895383	E067	14128
chr2	198905291	198905433	E067	24108
chr2	198918578	198918696	E067	37395
chr2	198860594	198860652	E068	-20531
chr2	198861601	198861700	E068	-19483
chr2	198861897	198861982	E068	-19201
chr2	198869628	198869727	E068	-11456
chr2	198869765	198869846	E068	-11337
chr2	198894292	198894356	E068	13109
chr2	198905291	198905433	E068	24108
chr2	198905500	198905702	E068	24317
chr2	198919509	198919737	E068	38326
chr2	198919820	198920207	E068	38637
chr2	198920560	198920776	E068	39377
chr2	198922587	198922655	E068	41404
chr2	198930117	198930438	E068	48934
chr2	198836717	198837189	E069	-43994
chr2	198837363	198837407	E069	-43776
chr2	198849914	198850263	E069	-30920
chr2	198860594	198860652	E069	-20531
chr2	198861601	198861700	E069	-19483
chr2	198869765	198869846	E069	-11337
chr2	198870058	198870605	E069	-10578
chr2	198881929	198882001	E069	746
chr2	198895156	198895261	E069	13973
chr2	198895311	198895383	E069	14128
chr2	198895428	198895521	E069	14245
chr2	198902752	198902963	E069	21569
chr2	198905291	198905433	E069	24108
chr2	198905500	198905702	E069	24317
chr2	198906774	198907233	E069	25591
chr2	198917564	198917745	E069	36381
chr2	198917974	198918065	E069	36791
chr2	198918578	198918696	E069	37395
chr2	198930117	198930438	E069	48934
chr2	198894809	198894947	E070	13626
chr2	198896952	198897006	E070	15769
chr2	198898314	198898364	E070	17131
chr2	198920560	198920776	E070	39377
chr2	198836417	198836461	E071	-44722
chr2	198836717	198837189	E071	-43994
chr2	198837363	198837407	E071	-43776
chr2	198838668	198838761	E071	-42422
chr2	198849914	198850263	E071	-30920
chr2	198858638	198858821	E071	-22362
chr2	198860594	198860652	E071	-20531
chr2	198861601	198861700	E071	-19483
chr2	198861897	198861982	E071	-19201
chr2	198862039	198862206	E071	-18977
chr2	198862262	198862312	E071	-18871
chr2	198869003	198869098	E071	-12085
chr2	198869628	198869727	E071	-11456
chr2	198869765	198869846	E071	-11337
chr2	198894292	198894356	E071	13109
chr2	198894442	198894522	E071	13259
chr2	198894809	198894947	E071	13626
chr2	198902752	198902963	E071	21569
chr2	198903313	198903359	E071	22130
chr2	198905291	198905433	E071	24108
chr2	198905500	198905702	E071	24317
chr2	198906774	198907233	E071	25591
chr2	198917564	198917745	E071	36381
chr2	198917974	198918065	E071	36791
chr2	198918578	198918696	E071	37395
chr2	198919150	198919308	E071	37967
chr2	198919509	198919737	E071	38326
chr2	198919820	198920207	E071	38637
chr2	198920560	198920776	E071	39377
chr2	198925168	198925266	E071	43985
chr2	198930117	198930438	E071	48934
chr2	198836717	198837189	E072	-43994
chr2	198837363	198837407	E072	-43776
chr2	198838668	198838761	E072	-42422
chr2	198849914	198850263	E072	-30920
chr2	198860594	198860652	E072	-20531
chr2	198861601	198861700	E072	-19483
chr2	198861897	198861982	E072	-19201
chr2	198862039	198862206	E072	-18977
chr2	198862262	198862312	E072	-18871
chr2	198870058	198870605	E072	-10578
chr2	198881929	198882001	E072	746
chr2	198895428	198895521	E072	14245
chr2	198902752	198902963	E072	21569
chr2	198905291	198905433	E072	24108
chr2	198905500	198905702	E072	24317
chr2	198914419	198914505	E072	33236
chr2	198917974	198918065	E072	36791
chr2	198918578	198918696	E072	37395
chr2	198919150	198919308	E072	37967
chr2	198919509	198919737	E072	38326
chr2	198919820	198920207	E072	38637
chr2	198920560	198920776	E072	39377
chr2	198922587	198922655	E072	41404
chr2	198925168	198925266	E072	43985
chr2	198860594	198860652	E073	-20531
chr2	198861601	198861700	E073	-19483
chr2	198869628	198869727	E073	-11456
chr2	198869765	198869846	E073	-11337
chr2	198870058	198870605	E073	-10578
chr2	198918578	198918696	E073	37395
chr2	198919150	198919308	E073	37967
chr2	198919509	198919737	E073	38326
chr2	198849914	198850263	E074	-30920
chr2	198860594	198860652	E074	-20531
chr2	198861601	198861700	E074	-19483
chr2	198861897	198861982	E074	-19201
chr2	198862039	198862206	E074	-18977
chr2	198862262	198862312	E074	-18871
chr2	198863014	198863054	E074	-18129
chr2	198868844	198868923	E074	-12260
chr2	198869003	198869098	E074	-12085
chr2	198869628	198869727	E074	-11456
chr2	198869765	198869846	E074	-11337
chr2	198881929	198882001	E074	746
chr2	198894292	198894356	E074	13109
chr2	198894442	198894522	E074	13259
chr2	198894809	198894947	E074	13626
chr2	198895156	198895261	E074	13973
chr2	198895311	198895383	E074	14128
chr2	198902752	198902963	E074	21569
chr2	198905291	198905433	E074	24108
chr2	198905500	198905702	E074	24317
chr2	198906774	198907233	E074	25591
chr2	198917564	198917745	E074	36381
chr2	198917974	198918065	E074	36791
chr2	198918578	198918696	E074	37395
chr2	198919150	198919308	E074	37967
chr2	198919509	198919737	E074	38326
chr2	198919820	198920207	E074	38637
chr2	198920560	198920776	E074	39377
chr2	198930117	198930438	E074	48934
chr2	198849914	198850263	E082	-30920