rs10196612

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0467 (13981/29896,GnomAD)
C=0498 (14500/29118,TOPMED)
C=0454 (2274/5008,1000G)
T==0494 (1903/3854,ALSPAC)
C=0497 (1842/3708,TWINSUK)

Position: chr2:198029415 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 133 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.198029415T>C
GRCh37.p13 chr 2	NC_000002.11:g.198894139T>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 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	T=0.491	C=0.509
1000Genomes	American	Sub	694	T=0.570	C=0.430
1000Genomes	East Asian	Sub	1008	T=0.780	C=0.220
1000Genomes	Europe	Sub	1006	T=0.454	C=0.546
1000Genomes	Global	Study-wide	5008	T=0.546	C=0.454
1000Genomes	South Asian	Sub	978	T=0.450	C=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.494	C=0.506
The Genome Aggregation Database	African	Sub	8694	T=0.479	C=0.521
The Genome Aggregation Database	American	Sub	836	T=0.650	C=0.350
The Genome Aggregation Database	East Asian	Sub	1616	T=0.802	C=0.198
The Genome Aggregation Database	Europe	Sub	18448	T=0.529	C=0.470
The Genome Aggregation Database	Global	Study-wide	29896	T=0.532	C=0.467
The Genome Aggregation Database	Other	Sub	302	T=0.480	C=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.502	C=0.498
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.503	C=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
rs10196612	1.18E-05	alcohol consumption	23743675

eQTL of rs10196612 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:198894139	SF3B1	ENSG00000115524.11	T>C	7.6222e-4	594324	Caudate_basal_ganglia

meQTL of rs10196612 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	-43876
chr2	198859584	198859710	E067	-34429
chr2	198860594	198860652	E067	-33487
chr2	198861601	198861700	E067	-32439
chr2	198861897	198861982	E067	-32157
chr2	198862039	198862206	E067	-31933
chr2	198862262	198862312	E067	-31827
chr2	198863014	198863054	E067	-31085
chr2	198895311	198895383	E067	1172
chr2	198905291	198905433	E067	11152
chr2	198918578	198918696	E067	24439
chr2	198860594	198860652	E068	-33487
chr2	198861601	198861700	E068	-32439
chr2	198861897	198861982	E068	-32157
chr2	198869628	198869727	E068	-24412
chr2	198869765	198869846	E068	-24293
chr2	198894292	198894356	E068	153
chr2	198905291	198905433	E068	11152
chr2	198905500	198905702	E068	11361
chr2	198919509	198919737	E068	25370
chr2	198919820	198920207	E068	25681
chr2	198920560	198920776	E068	26421
chr2	198922587	198922655	E068	28448
chr2	198930117	198930438	E068	35978
chr2	198849914	198850263	E069	-43876
chr2	198860594	198860652	E069	-33487
chr2	198861601	198861700	E069	-32439
chr2	198869765	198869846	E069	-24293
chr2	198870058	198870605	E069	-23534
chr2	198881929	198882001	E069	-12138
chr2	198895156	198895261	E069	1017
chr2	198895311	198895383	E069	1172
chr2	198895428	198895521	E069	1289
chr2	198902752	198902963	E069	8613
chr2	198905291	198905433	E069	11152
chr2	198905500	198905702	E069	11361
chr2	198906774	198907233	E069	12635
chr2	198917564	198917745	E069	23425
chr2	198917974	198918065	E069	23835
chr2	198918578	198918696	E069	24439
chr2	198930117	198930438	E069	35978
chr2	198894809	198894947	E070	670
chr2	198896952	198897006	E070	2813
chr2	198898314	198898364	E070	4175
chr2	198920560	198920776	E070	26421
chr2	198849914	198850263	E071	-43876
chr2	198858638	198858821	E071	-35318
chr2	198860594	198860652	E071	-33487
chr2	198861601	198861700	E071	-32439
chr2	198861897	198861982	E071	-32157
chr2	198862039	198862206	E071	-31933
chr2	198862262	198862312	E071	-31827
chr2	198869003	198869098	E071	-25041
chr2	198869628	198869727	E071	-24412
chr2	198869765	198869846	E071	-24293
chr2	198894292	198894356	E071	153
chr2	198894442	198894522	E071	303
chr2	198894809	198894947	E071	670
chr2	198902752	198902963	E071	8613
chr2	198903313	198903359	E071	9174
chr2	198905291	198905433	E071	11152
chr2	198905500	198905702	E071	11361
chr2	198906774	198907233	E071	12635
chr2	198917564	198917745	E071	23425
chr2	198917974	198918065	E071	23835
chr2	198918578	198918696	E071	24439
chr2	198919150	198919308	E071	25011
chr2	198919509	198919737	E071	25370
chr2	198919820	198920207	E071	25681
chr2	198920560	198920776	E071	26421
chr2	198925168	198925266	E071	31029
chr2	198930117	198930438	E071	35978
chr2	198931481	198931548	E071	37342
chr2	198849914	198850263	E072	-43876
chr2	198860594	198860652	E072	-33487
chr2	198861601	198861700	E072	-32439
chr2	198861897	198861982	E072	-32157
chr2	198862039	198862206	E072	-31933
chr2	198862262	198862312	E072	-31827
chr2	198870058	198870605	E072	-23534
chr2	198881929	198882001	E072	-12138
chr2	198895428	198895521	E072	1289
chr2	198902752	198902963	E072	8613
chr2	198905291	198905433	E072	11152
chr2	198905500	198905702	E072	11361
chr2	198914419	198914505	E072	20280
chr2	198917974	198918065	E072	23835
chr2	198918578	198918696	E072	24439
chr2	198919150	198919308	E072	25011
chr2	198919509	198919737	E072	25370
chr2	198919820	198920207	E072	25681
chr2	198920560	198920776	E072	26421
chr2	198922587	198922655	E072	28448
chr2	198925168	198925266	E072	31029
chr2	198860594	198860652	E073	-33487
chr2	198861601	198861700	E073	-32439
chr2	198869628	198869727	E073	-24412
chr2	198869765	198869846	E073	-24293
chr2	198870058	198870605	E073	-23534
chr2	198918578	198918696	E073	24439
chr2	198919150	198919308	E073	25011
chr2	198919509	198919737	E073	25370
chr2	198849914	198850263	E074	-43876
chr2	198860594	198860652	E074	-33487
chr2	198861601	198861700	E074	-32439
chr2	198861897	198861982	E074	-32157
chr2	198862039	198862206	E074	-31933
chr2	198862262	198862312	E074	-31827
chr2	198863014	198863054	E074	-31085
chr2	198868844	198868923	E074	-25216
chr2	198869003	198869098	E074	-25041
chr2	198869628	198869727	E074	-24412
chr2	198869765	198869846	E074	-24293
chr2	198881929	198882001	E074	-12138
chr2	198894292	198894356	E074	153
chr2	198894442	198894522	E074	303
chr2	198894809	198894947	E074	670
chr2	198895156	198895261	E074	1017
chr2	198895311	198895383	E074	1172
chr2	198902752	198902963	E074	8613
chr2	198905291	198905433	E074	11152
chr2	198905500	198905702	E074	11361
chr2	198906774	198907233	E074	12635
chr2	198917564	198917745	E074	23425
chr2	198917974	198918065	E074	23835
chr2	198918578	198918696	E074	24439
chr2	198919150	198919308	E074	25011
chr2	198919509	198919737	E074	25370
chr2	198919820	198920207	E074	25681
chr2	198920560	198920776	E074	26421
chr2	198930117	198930438	E074	35978
chr2	198931481	198931548	E074	37342
chr2	198849914	198850263	E082	-43876