rs9973400

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0494 (14779/29916,GnomAD)
T==0441 (12848/29118,TOPMED)
T==0497 (2491/5008,1000G)
T==0481 (1855/3854,ALSPAC)
T==0490 (1817/3708,TWINSUK)

Position: chr2:198076854 (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.198076854T>C
GRCh37.p13 chr 2	NC_000002.11:g.198941578T>C

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 X4	XM_005246644.3: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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.369	C=0.631
1000Genomes	American	Sub	694	T=0.550	C=0.450
1000Genomes	East Asian	Sub	1008	T=0.774	C=0.226
1000Genomes	Europe	Sub	1006	T=0.449	C=0.551
1000Genomes	Global	Study-wide	5008	T=0.497	C=0.503
1000Genomes	South Asian	Sub	978	T=0.400	C=0.600
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.481	C=0.519
The Genome Aggregation Database	African	Sub	8694	T=0.375	C=0.625
The Genome Aggregation Database	American	Sub	828	T=0.640	C=0.360
The Genome Aggregation Database	East Asian	Sub	1620	T=0.804	C=0.196
The Genome Aggregation Database	Europe	Sub	18472	T=0.516	C=0.483
The Genome Aggregation Database	Global	Study-wide	29916	T=0.494	C=0.506
The Genome Aggregation Database	Other	Sub	302	T=0.470	C=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.441	C=0.558
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.490	C=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
rs9973400	8.29E-06	alcohol consumption	23743675

eQTL of rs9973400 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 rs9973400 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	198895311	198895383	E067	-46195
chr2	198905291	198905433	E067	-36145
chr2	198918578	198918696	E067	-22882
chr2	198945273	198945529	E067	3695
chr2	198961450	198961502	E067	19872
chr2	198961841	198961912	E067	20263
chr2	198962411	198962470	E067	20833
chr2	198963763	198963935	E067	22185
chr2	198965149	198965308	E067	23571
chr2	198975540	198975603	E067	33962
chr2	198978077	198978371	E067	36499
chr2	198894292	198894356	E068	-47222
chr2	198905291	198905433	E068	-36145
chr2	198905500	198905702	E068	-35876
chr2	198919509	198919737	E068	-21841
chr2	198919820	198920207	E068	-21371
chr2	198920560	198920776	E068	-20802
chr2	198922587	198922655	E068	-18923
chr2	198930117	198930438	E068	-11140
chr2	198945273	198945529	E068	3695
chr2	198961841	198961912	E068	20263
chr2	198965149	198965308	E068	23571
chr2	198895156	198895261	E069	-46317
chr2	198895311	198895383	E069	-46195
chr2	198895428	198895521	E069	-46057
chr2	198902752	198902963	E069	-38615
chr2	198905291	198905433	E069	-36145
chr2	198905500	198905702	E069	-35876
chr2	198906774	198907233	E069	-34345
chr2	198917564	198917745	E069	-23833
chr2	198917974	198918065	E069	-23513
chr2	198918578	198918696	E069	-22882
chr2	198930117	198930438	E069	-11140
chr2	198945273	198945529	E069	3695
chr2	198961841	198961912	E069	20263
chr2	198962411	198962470	E069	20833
chr2	198963763	198963935	E069	22185
chr2	198965149	198965308	E069	23571
chr2	198975540	198975603	E069	33962
chr2	198978425	198978498	E069	36847
chr2	198989790	198989843	E069	48212
chr2	198989886	198989996	E069	48308
chr2	198894809	198894947	E070	-46631
chr2	198896952	198897006	E070	-44572
chr2	198898314	198898364	E070	-43214
chr2	198920560	198920776	E070	-20802
chr2	198894292	198894356	E071	-47222
chr2	198894442	198894522	E071	-47056
chr2	198894809	198894947	E071	-46631
chr2	198902752	198902963	E071	-38615
chr2	198903313	198903359	E071	-38219
chr2	198905291	198905433	E071	-36145
chr2	198905500	198905702	E071	-35876
chr2	198906774	198907233	E071	-34345
chr2	198917564	198917745	E071	-23833
chr2	198917974	198918065	E071	-23513
chr2	198918578	198918696	E071	-22882
chr2	198919150	198919308	E071	-22270
chr2	198919509	198919737	E071	-21841
chr2	198919820	198920207	E071	-21371
chr2	198920560	198920776	E071	-20802
chr2	198925168	198925266	E071	-16312
chr2	198930117	198930438	E071	-11140
chr2	198931481	198931548	E071	-10030
chr2	198945273	198945529	E071	3695
chr2	198960865	198960964	E071	19287
chr2	198961450	198961502	E071	19872
chr2	198961841	198961912	E071	20263
chr2	198962411	198962470	E071	20833
chr2	198963763	198963935	E071	22185
chr2	198965149	198965308	E071	23571
chr2	198975540	198975603	E071	33962
chr2	198977050	198977114	E071	35472
chr2	198981402	198981945	E071	39824
chr2	198982067	198982154	E071	40489
chr2	198982183	198982417	E071	40605
chr2	198895428	198895521	E072	-46057
chr2	198902752	198902963	E072	-38615
chr2	198905291	198905433	E072	-36145
chr2	198905500	198905702	E072	-35876
chr2	198914419	198914505	E072	-27073
chr2	198917974	198918065	E072	-23513
chr2	198918578	198918696	E072	-22882
chr2	198919150	198919308	E072	-22270
chr2	198919509	198919737	E072	-21841
chr2	198919820	198920207	E072	-21371
chr2	198920560	198920776	E072	-20802
chr2	198922587	198922655	E072	-18923
chr2	198925168	198925266	E072	-16312
chr2	198945273	198945529	E072	3695
chr2	198961841	198961912	E072	20263
chr2	198962411	198962470	E072	20833
chr2	198965149	198965308	E072	23571
chr2	198975540	198975603	E072	33962
chr2	198977050	198977114	E072	35472
chr2	198978077	198978371	E072	36499
chr2	198989790	198989843	E072	48212
chr2	198989886	198989996	E072	48308
chr2	198918578	198918696	E073	-22882
chr2	198919150	198919308	E073	-22270
chr2	198919509	198919737	E073	-21841
chr2	198962411	198962470	E073	20833
chr2	198965149	198965308	E073	23571
chr2	198894292	198894356	E074	-47222
chr2	198894442	198894522	E074	-47056
chr2	198894809	198894947	E074	-46631
chr2	198895156	198895261	E074	-46317
chr2	198895311	198895383	E074	-46195
chr2	198902752	198902963	E074	-38615
chr2	198905291	198905433	E074	-36145
chr2	198905500	198905702	E074	-35876
chr2	198906774	198907233	E074	-34345
chr2	198917564	198917745	E074	-23833
chr2	198917974	198918065	E074	-23513
chr2	198918578	198918696	E074	-22882
chr2	198919150	198919308	E074	-22270
chr2	198919509	198919737	E074	-21841
chr2	198919820	198920207	E074	-21371
chr2	198920560	198920776	E074	-20802
chr2	198930117	198930438	E074	-11140
chr2	198931481	198931548	E074	-10030
chr2	198945273	198945529	E074	3695
chr2	198961841	198961912	E074	20263
chr2	198962411	198962470	E074	20833
chr2	198963763	198963935	E074	22185
chr2	198965149	198965308	E074	23571
chr2	198975540	198975603	E074	33962
chr2	198978077	198978371	E074	36499
chr2	198978425	198978498	E074	36847
chr2	198978866	198979373	E074	37288
chr2	198979410	198979460	E074	37832
chr2	198979807	198979926	E074	38229
chr2	198980083	198980143	E074	38505
chr2	198984220	198984270	E074	42642
chr2	198945273	198945529	E081	3695