rs11690149

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0407 (11983/29378,GnomAD)
T=0399 (11634/29118,TOPMED)
T=0385 (1930/5008,1000G)
C==0483 (1863/3854,ALSPAC)
C==0490 (1817/3708,TWINSUK)

Position: chr2:198069080 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 130 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.198069080C>T
GRCh37.p13 chr 2	NC_000002.11:g.198933804C>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=0.768	T=0.232
1000Genomes	American	Sub	694	C=0.590	T=0.410
1000Genomes	East Asian	Sub	1008	C=0.778	T=0.222
1000Genomes	Europe	Sub	1006	C=0.449	T=0.551
1000Genomes	Global	Study-wide	5008	C=0.615	T=0.385
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=0.483	T=0.517
The Genome Aggregation Database	African	Sub	8622	C=0.717	T=0.283
The Genome Aggregation Database	American	Sub	792	C=0.660	T=0.340
The Genome Aggregation Database	East Asian	Sub	1614	C=0.804	T=0.196
The Genome Aggregation Database	Europe	Sub	18050	C=0.512	T=0.487
The Genome Aggregation Database	Global	Study-wide	29378	C=0.592	T=0.407
The Genome Aggregation Database	Other	Sub	300	C=0.480	T=0.520
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.600	T=0.399
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
rs11690149	6.18E-06	alcohol consumption	23743675

eQTL of rs11690149 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 rs11690149 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	-38421
chr2	198905291	198905433	E067	-28371
chr2	198918578	198918696	E067	-15108
chr2	198945273	198945529	E067	11469
chr2	198961450	198961502	E067	27646
chr2	198961841	198961912	E067	28037
chr2	198962411	198962470	E067	28607
chr2	198963763	198963935	E067	29959
chr2	198965149	198965308	E067	31345
chr2	198975540	198975603	E067	41736
chr2	198978077	198978371	E067	44273
chr2	198894292	198894356	E068	-39448
chr2	198905291	198905433	E068	-28371
chr2	198905500	198905702	E068	-28102
chr2	198919509	198919737	E068	-14067
chr2	198919820	198920207	E068	-13597
chr2	198920560	198920776	E068	-13028
chr2	198922587	198922655	E068	-11149
chr2	198930117	198930438	E068	-3366
chr2	198945273	198945529	E068	11469
chr2	198961841	198961912	E068	28037
chr2	198965149	198965308	E068	31345
chr2	198895156	198895261	E069	-38543
chr2	198895311	198895383	E069	-38421
chr2	198895428	198895521	E069	-38283
chr2	198902752	198902963	E069	-30841
chr2	198905291	198905433	E069	-28371
chr2	198905500	198905702	E069	-28102
chr2	198906774	198907233	E069	-26571
chr2	198917564	198917745	E069	-16059
chr2	198917974	198918065	E069	-15739
chr2	198918578	198918696	E069	-15108
chr2	198930117	198930438	E069	-3366
chr2	198945273	198945529	E069	11469
chr2	198961841	198961912	E069	28037
chr2	198962411	198962470	E069	28607
chr2	198963763	198963935	E069	29959
chr2	198965149	198965308	E069	31345
chr2	198975540	198975603	E069	41736
chr2	198978425	198978498	E069	44621
chr2	198894809	198894947	E070	-38857
chr2	198896952	198897006	E070	-36798
chr2	198898314	198898364	E070	-35440
chr2	198920560	198920776	E070	-13028
chr2	198894292	198894356	E071	-39448
chr2	198894442	198894522	E071	-39282
chr2	198894809	198894947	E071	-38857
chr2	198902752	198902963	E071	-30841
chr2	198903313	198903359	E071	-30445
chr2	198905291	198905433	E071	-28371
chr2	198905500	198905702	E071	-28102
chr2	198906774	198907233	E071	-26571
chr2	198917564	198917745	E071	-16059
chr2	198917974	198918065	E071	-15739
chr2	198918578	198918696	E071	-15108
chr2	198919150	198919308	E071	-14496
chr2	198919509	198919737	E071	-14067
chr2	198919820	198920207	E071	-13597
chr2	198920560	198920776	E071	-13028
chr2	198925168	198925266	E071	-8538
chr2	198930117	198930438	E071	-3366
chr2	198931481	198931548	E071	-2256
chr2	198945273	198945529	E071	11469
chr2	198960865	198960964	E071	27061
chr2	198961450	198961502	E071	27646
chr2	198961841	198961912	E071	28037
chr2	198962411	198962470	E071	28607
chr2	198963763	198963935	E071	29959
chr2	198965149	198965308	E071	31345
chr2	198975540	198975603	E071	41736
chr2	198977050	198977114	E071	43246
chr2	198981402	198981945	E071	47598
chr2	198982067	198982154	E071	48263
chr2	198982183	198982417	E071	48379
chr2	198895428	198895521	E072	-38283
chr2	198902752	198902963	E072	-30841
chr2	198905291	198905433	E072	-28371
chr2	198905500	198905702	E072	-28102
chr2	198914419	198914505	E072	-19299
chr2	198917974	198918065	E072	-15739
chr2	198918578	198918696	E072	-15108
chr2	198919150	198919308	E072	-14496
chr2	198919509	198919737	E072	-14067
chr2	198919820	198920207	E072	-13597
chr2	198920560	198920776	E072	-13028
chr2	198922587	198922655	E072	-11149
chr2	198925168	198925266	E072	-8538
chr2	198945273	198945529	E072	11469
chr2	198961841	198961912	E072	28037
chr2	198962411	198962470	E072	28607
chr2	198965149	198965308	E072	31345
chr2	198975540	198975603	E072	41736
chr2	198977050	198977114	E072	43246
chr2	198978077	198978371	E072	44273
chr2	198918578	198918696	E073	-15108
chr2	198919150	198919308	E073	-14496
chr2	198919509	198919737	E073	-14067
chr2	198962411	198962470	E073	28607
chr2	198965149	198965308	E073	31345
chr2	198894292	198894356	E074	-39448
chr2	198894442	198894522	E074	-39282
chr2	198894809	198894947	E074	-38857
chr2	198895156	198895261	E074	-38543
chr2	198895311	198895383	E074	-38421
chr2	198902752	198902963	E074	-30841
chr2	198905291	198905433	E074	-28371
chr2	198905500	198905702	E074	-28102
chr2	198906774	198907233	E074	-26571
chr2	198917564	198917745	E074	-16059
chr2	198917974	198918065	E074	-15739
chr2	198918578	198918696	E074	-15108
chr2	198919150	198919308	E074	-14496
chr2	198919509	198919737	E074	-14067
chr2	198919820	198920207	E074	-13597
chr2	198920560	198920776	E074	-13028
chr2	198930117	198930438	E074	-3366
chr2	198931481	198931548	E074	-2256
chr2	198945273	198945529	E074	11469
chr2	198961841	198961912	E074	28037
chr2	198962411	198962470	E074	28607
chr2	198963763	198963935	E074	29959
chr2	198965149	198965308	E074	31345
chr2	198975540	198975603	E074	41736
chr2	198978077	198978371	E074	44273
chr2	198978425	198978498	E074	44621
chr2	198978866	198979373	E074	45062
chr2	198979410	198979460	E074	45606
chr2	198979807	198979926	E074	46003
chr2	198980083	198980143	E074	46279
chr2	198945273	198945529	E081	11469