rs9712275

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0440 (13177/29916,GnomAD)
T=0446 (12995/29118,TOPMED)
T=0422 (2114/5008,1000G)
C==0480 (1851/3854,ALSPAC)
C==0490 (1817/3708,TWINSUK)

Position: chr2:198042419 (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.198042419C>T
GRCh37.p13 chr 2	NC_000002.11:g.198907143C>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	C=0.644	T=0.356
1000Genomes	American	Sub	694	C=0.580	T=0.420
1000Genomes	East Asian	Sub	1008	C=0.779	T=0.221
1000Genomes	Europe	Sub	1006	C=0.438	T=0.562
1000Genomes	Global	Study-wide	5008	C=0.578	T=0.422
1000Genomes	South Asian	Sub	978	C=0.430	T=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.480	T=0.520
The Genome Aggregation Database	African	Sub	8706	C=0.620	T=0.380
The Genome Aggregation Database	American	Sub	836	C=0.650	T=0.350
The Genome Aggregation Database	East Asian	Sub	1616	C=0.801	T=0.199
The Genome Aggregation Database	Europe	Sub	18456	C=0.507	T=0.492
The Genome Aggregation Database	Global	Study-wide	29916	C=0.559	T=0.440
The Genome Aggregation Database	Other	Sub	302	C=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.553	T=0.446
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.490	T=0.510

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
rs9712275	5.77E-06	alcohol consumption	23743675

eQTL of rs9712275 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 rs9712275 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	-47433
chr2	198860594	198860652	E067	-46491
chr2	198861601	198861700	E067	-45443
chr2	198861897	198861982	E067	-45161
chr2	198862039	198862206	E067	-44937
chr2	198862262	198862312	E067	-44831
chr2	198863014	198863054	E067	-44089
chr2	198895311	198895383	E067	-11760
chr2	198905291	198905433	E067	-1710
chr2	198918578	198918696	E067	11435
chr2	198945273	198945529	E067	38130
chr2	198860594	198860652	E068	-46491
chr2	198861601	198861700	E068	-45443
chr2	198861897	198861982	E068	-45161
chr2	198869628	198869727	E068	-37416
chr2	198869765	198869846	E068	-37297
chr2	198894292	198894356	E068	-12787
chr2	198905291	198905433	E068	-1710
chr2	198905500	198905702	E068	-1441
chr2	198919509	198919737	E068	12366
chr2	198919820	198920207	E068	12677
chr2	198920560	198920776	E068	13417
chr2	198922587	198922655	E068	15444
chr2	198930117	198930438	E068	22974
chr2	198945273	198945529	E068	38130
chr2	198860594	198860652	E069	-46491
chr2	198861601	198861700	E069	-45443
chr2	198869765	198869846	E069	-37297
chr2	198870058	198870605	E069	-36538
chr2	198881929	198882001	E069	-25142
chr2	198895156	198895261	E069	-11882
chr2	198895311	198895383	E069	-11760
chr2	198895428	198895521	E069	-11622
chr2	198902752	198902963	E069	-4180
chr2	198905291	198905433	E069	-1710
chr2	198905500	198905702	E069	-1441
chr2	198906774	198907233	E069	0
chr2	198917564	198917745	E069	10421
chr2	198917974	198918065	E069	10831
chr2	198918578	198918696	E069	11435
chr2	198930117	198930438	E069	22974
chr2	198945273	198945529	E069	38130
chr2	198894809	198894947	E070	-12196
chr2	198896952	198897006	E070	-10137
chr2	198898314	198898364	E070	-8779
chr2	198920560	198920776	E070	13417
chr2	198858638	198858821	E071	-48322
chr2	198860594	198860652	E071	-46491
chr2	198861601	198861700	E071	-45443
chr2	198861897	198861982	E071	-45161
chr2	198862039	198862206	E071	-44937
chr2	198862262	198862312	E071	-44831
chr2	198869003	198869098	E071	-38045
chr2	198869628	198869727	E071	-37416
chr2	198869765	198869846	E071	-37297
chr2	198894292	198894356	E071	-12787
chr2	198894442	198894522	E071	-12621
chr2	198894809	198894947	E071	-12196
chr2	198902752	198902963	E071	-4180
chr2	198903313	198903359	E071	-3784
chr2	198905291	198905433	E071	-1710
chr2	198905500	198905702	E071	-1441
chr2	198906774	198907233	E071	0
chr2	198917564	198917745	E071	10421
chr2	198917974	198918065	E071	10831
chr2	198918578	198918696	E071	11435
chr2	198919150	198919308	E071	12007
chr2	198919509	198919737	E071	12366
chr2	198919820	198920207	E071	12677
chr2	198920560	198920776	E071	13417
chr2	198925168	198925266	E071	18025
chr2	198930117	198930438	E071	22974
chr2	198931481	198931548	E071	24338
chr2	198945273	198945529	E071	38130
chr2	198860594	198860652	E072	-46491
chr2	198861601	198861700	E072	-45443
chr2	198861897	198861982	E072	-45161
chr2	198862039	198862206	E072	-44937
chr2	198862262	198862312	E072	-44831
chr2	198870058	198870605	E072	-36538
chr2	198881929	198882001	E072	-25142
chr2	198895428	198895521	E072	-11622
chr2	198902752	198902963	E072	-4180
chr2	198905291	198905433	E072	-1710
chr2	198905500	198905702	E072	-1441
chr2	198914419	198914505	E072	7276
chr2	198917974	198918065	E072	10831
chr2	198918578	198918696	E072	11435
chr2	198919150	198919308	E072	12007
chr2	198919509	198919737	E072	12366
chr2	198919820	198920207	E072	12677
chr2	198920560	198920776	E072	13417
chr2	198922587	198922655	E072	15444
chr2	198925168	198925266	E072	18025
chr2	198945273	198945529	E072	38130
chr2	198860594	198860652	E073	-46491
chr2	198861601	198861700	E073	-45443
chr2	198869628	198869727	E073	-37416
chr2	198869765	198869846	E073	-37297
chr2	198870058	198870605	E073	-36538
chr2	198918578	198918696	E073	11435
chr2	198919150	198919308	E073	12007
chr2	198919509	198919737	E073	12366
chr2	198860594	198860652	E074	-46491
chr2	198861601	198861700	E074	-45443
chr2	198861897	198861982	E074	-45161
chr2	198862039	198862206	E074	-44937
chr2	198862262	198862312	E074	-44831
chr2	198863014	198863054	E074	-44089
chr2	198868844	198868923	E074	-38220
chr2	198869003	198869098	E074	-38045
chr2	198869628	198869727	E074	-37416
chr2	198869765	198869846	E074	-37297
chr2	198881929	198882001	E074	-25142
chr2	198894292	198894356	E074	-12787
chr2	198894442	198894522	E074	-12621
chr2	198894809	198894947	E074	-12196
chr2	198895156	198895261	E074	-11882
chr2	198895311	198895383	E074	-11760
chr2	198902752	198902963	E074	-4180
chr2	198905291	198905433	E074	-1710
chr2	198905500	198905702	E074	-1441
chr2	198906774	198907233	E074	0
chr2	198917564	198917745	E074	10421
chr2	198917974	198918065	E074	10831
chr2	198918578	198918696	E074	11435
chr2	198919150	198919308	E074	12007
chr2	198919509	198919737	E074	12366
chr2	198919820	198920207	E074	12677
chr2	198920560	198920776	E074	13417
chr2	198930117	198930438	E074	22974
chr2	198931481	198931548	E074	24338
chr2	198945273	198945529	E074	38130
chr2	198945273	198945529	E081	38130