rs2139049

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0462 (13811/29890,GnomAD)
A=0488 (14212/29118,TOPMED)
A=0449 (2250/5008,1000G)
G==0494 (1903/3854,ALSPAC)
A=0497 (1843/3708,TWINSUK)

Position: chr2:198022936 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 135 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.198022936G>A
GRCh37.p13 chr 2	NC_000002.11:g.198887660G>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=0.507	A=0.493
1000Genomes	American	Sub	694	G=0.580	A=0.420
1000Genomes	East Asian	Sub	1008	G=0.780	A=0.220
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	8690	G=0.497	A=0.503
The Genome Aggregation Database	American	Sub	834	G=0.660	A=0.340
The Genome Aggregation Database	East Asian	Sub	1616	G=0.803	A=0.197
The Genome Aggregation Database	Europe	Sub	18448	G=0.529	A=0.470
The Genome Aggregation Database	Global	Study-wide	29890	G=0.537	A=0.462
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
rs2139049	1.21E-05	alcohol consumption	23743675

eQTL of rs2139049 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:198887660	SF3B1	ENSG00000115524.11	G>A	7.6222e-4	587845	Caudate_basal_ganglia

meQTL of rs2139049 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	-37397
chr2	198859584	198859710	E067	-27950
chr2	198860594	198860652	E067	-27008
chr2	198861601	198861700	E067	-25960
chr2	198861897	198861982	E067	-25678
chr2	198862039	198862206	E067	-25454
chr2	198862262	198862312	E067	-25348
chr2	198863014	198863054	E067	-24606
chr2	198895311	198895383	E067	7651
chr2	198905291	198905433	E067	17631
chr2	198918578	198918696	E067	30918
chr2	198860594	198860652	E068	-27008
chr2	198861601	198861700	E068	-25960
chr2	198861897	198861982	E068	-25678
chr2	198869628	198869727	E068	-17933
chr2	198869765	198869846	E068	-17814
chr2	198894292	198894356	E068	6632
chr2	198905291	198905433	E068	17631
chr2	198905500	198905702	E068	17840
chr2	198919509	198919737	E068	31849
chr2	198919820	198920207	E068	32160
chr2	198920560	198920776	E068	32900
chr2	198922587	198922655	E068	34927
chr2	198930117	198930438	E068	42457
chr2	198849914	198850263	E069	-37397
chr2	198860594	198860652	E069	-27008
chr2	198861601	198861700	E069	-25960
chr2	198869765	198869846	E069	-17814
chr2	198870058	198870605	E069	-17055
chr2	198881929	198882001	E069	-5659
chr2	198895156	198895261	E069	7496
chr2	198895311	198895383	E069	7651
chr2	198895428	198895521	E069	7768
chr2	198902752	198902963	E069	15092
chr2	198905291	198905433	E069	17631
chr2	198905500	198905702	E069	17840
chr2	198906774	198907233	E069	19114
chr2	198917564	198917745	E069	29904
chr2	198917974	198918065	E069	30314
chr2	198918578	198918696	E069	30918
chr2	198930117	198930438	E069	42457
chr2	198894809	198894947	E070	7149
chr2	198896952	198897006	E070	9292
chr2	198898314	198898364	E070	10654
chr2	198920560	198920776	E070	32900
chr2	198838668	198838761	E071	-48899
chr2	198849914	198850263	E071	-37397
chr2	198858638	198858821	E071	-28839
chr2	198860594	198860652	E071	-27008
chr2	198861601	198861700	E071	-25960
chr2	198861897	198861982	E071	-25678
chr2	198862039	198862206	E071	-25454
chr2	198862262	198862312	E071	-25348
chr2	198869003	198869098	E071	-18562
chr2	198869628	198869727	E071	-17933
chr2	198869765	198869846	E071	-17814
chr2	198894292	198894356	E071	6632
chr2	198894442	198894522	E071	6782
chr2	198894809	198894947	E071	7149
chr2	198902752	198902963	E071	15092
chr2	198903313	198903359	E071	15653
chr2	198905291	198905433	E071	17631
chr2	198905500	198905702	E071	17840
chr2	198906774	198907233	E071	19114
chr2	198917564	198917745	E071	29904
chr2	198917974	198918065	E071	30314
chr2	198918578	198918696	E071	30918
chr2	198919150	198919308	E071	31490
chr2	198919509	198919737	E071	31849
chr2	198919820	198920207	E071	32160
chr2	198920560	198920776	E071	32900
chr2	198925168	198925266	E071	37508
chr2	198930117	198930438	E071	42457
chr2	198931481	198931548	E071	43821
chr2	198838668	198838761	E072	-48899
chr2	198849914	198850263	E072	-37397
chr2	198860594	198860652	E072	-27008
chr2	198861601	198861700	E072	-25960
chr2	198861897	198861982	E072	-25678
chr2	198862039	198862206	E072	-25454
chr2	198862262	198862312	E072	-25348
chr2	198870058	198870605	E072	-17055
chr2	198881929	198882001	E072	-5659
chr2	198895428	198895521	E072	7768
chr2	198902752	198902963	E072	15092
chr2	198905291	198905433	E072	17631
chr2	198905500	198905702	E072	17840
chr2	198914419	198914505	E072	26759
chr2	198917974	198918065	E072	30314
chr2	198918578	198918696	E072	30918
chr2	198919150	198919308	E072	31490
chr2	198919509	198919737	E072	31849
chr2	198919820	198920207	E072	32160
chr2	198920560	198920776	E072	32900
chr2	198922587	198922655	E072	34927
chr2	198925168	198925266	E072	37508
chr2	198860594	198860652	E073	-27008
chr2	198861601	198861700	E073	-25960
chr2	198869628	198869727	E073	-17933
chr2	198869765	198869846	E073	-17814
chr2	198870058	198870605	E073	-17055
chr2	198918578	198918696	E073	30918
chr2	198919150	198919308	E073	31490
chr2	198919509	198919737	E073	31849
chr2	198849914	198850263	E074	-37397
chr2	198860594	198860652	E074	-27008
chr2	198861601	198861700	E074	-25960
chr2	198861897	198861982	E074	-25678
chr2	198862039	198862206	E074	-25454
chr2	198862262	198862312	E074	-25348
chr2	198863014	198863054	E074	-24606
chr2	198868844	198868923	E074	-18737
chr2	198869003	198869098	E074	-18562
chr2	198869628	198869727	E074	-17933
chr2	198869765	198869846	E074	-17814
chr2	198881929	198882001	E074	-5659
chr2	198894292	198894356	E074	6632
chr2	198894442	198894522	E074	6782
chr2	198894809	198894947	E074	7149
chr2	198895156	198895261	E074	7496
chr2	198895311	198895383	E074	7651
chr2	198902752	198902963	E074	15092
chr2	198905291	198905433	E074	17631
chr2	198905500	198905702	E074	17840
chr2	198906774	198907233	E074	19114
chr2	198917564	198917745	E074	29904
chr2	198917974	198918065	E074	30314
chr2	198918578	198918696	E074	30918
chr2	198919150	198919308	E074	31490
chr2	198919509	198919737	E074	31849
chr2	198919820	198920207	E074	32160
chr2	198920560	198920776	E074	32900
chr2	198930117	198930438	E074	42457
chr2	198931481	198931548	E074	43821
chr2	198849914	198850263	E082	-37397