rs10180112

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

PLCL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0171 (5109/29852,GnomAD)
C==0200 (5833/29118,TOPMED)
C==0139 (694/5008,1000G)
C==0108 (417/3854,ALSPAC)
C==0110 (409/3708,TWINSUK)

Position: chr2:198118134 (GRCh38.p7) (2q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 125 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.198118134C>G
GRCh37.p13 chr 2	NC_000002.11:g.198982858C>G

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	C=0.367	G=0.633
1000Genomes	American	Sub	694	C=0.110	G=0.890
1000Genomes	East Asian	Sub	1008	C=0.000	G=1.000
1000Genomes	Europe	Sub	1006	C=0.099	G=0.901
1000Genomes	Global	Study-wide	5008	C=0.139	G=0.861
1000Genomes	South Asian	Sub	978	C=0.040	G=0.960
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.108	G=0.892
The Genome Aggregation Database	African	Sub	8700	C=0.321	G=0.679
The Genome Aggregation Database	American	Sub	838	C=0.080	G=0.920
The Genome Aggregation Database	East Asian	Sub	1548	C=0.000	G=1.000
The Genome Aggregation Database	Europe	Sub	18464	C=0.120	G=0.879
The Genome Aggregation Database	Global	Study-wide	29852	C=0.171	G=0.828
The Genome Aggregation Database	Other	Sub	302	C=0.080	G=0.920
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.200	G=0.799
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.110	G=0.890

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res
18776929	Identification of PLCL1 gene for hip bone size variation in females in a genome-wide association study.	Liu YZ	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs10180112	0.000522	alcohol dependence	21314694

eQTL of rs10180112 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 rs10180112 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	198945273	198945529	E067	-37329
chr2	198961450	198961502	E067	-21356
chr2	198961841	198961912	E067	-20946
chr2	198962411	198962470	E067	-20388
chr2	198963763	198963935	E067	-18923
chr2	198965149	198965308	E067	-17550
chr2	198975540	198975603	E067	-7255
chr2	198978077	198978371	E067	-4487
chr2	199009310	199009414	E067	26452
chr2	199009458	199009726	E067	26600
chr2	199010610	199010667	E067	27752
chr2	199010781	199010871	E067	27923
chr2	199011098	199011243	E067	28240
chr2	199011257	199011634	E067	28399
chr2	199025910	199026414	E067	43052
chr2	199026493	199026575	E067	43635
chr2	199026677	199026731	E067	43819
chr2	198945273	198945529	E068	-37329
chr2	198961841	198961912	E068	-20946
chr2	198965149	198965308	E068	-17550
chr2	199009310	199009414	E068	26452
chr2	199025910	199026414	E068	43052
chr2	199026493	199026575	E068	43635
chr2	199028379	199028419	E068	45521
chr2	198945273	198945529	E069	-37329
chr2	198961841	198961912	E069	-20946
chr2	198962411	198962470	E069	-20388
chr2	198963763	198963935	E069	-18923
chr2	198965149	198965308	E069	-17550
chr2	198975540	198975603	E069	-7255
chr2	198978425	198978498	E069	-4360
chr2	198989790	198989843	E069	6932
chr2	198989886	198989996	E069	7028
chr2	198998950	198999284	E069	16092
chr2	198999297	198999591	E069	16439
chr2	198999803	198999847	E069	16945
chr2	199000215	199000640	E069	17357
chr2	199002291	199002404	E069	19433
chr2	199009310	199009414	E069	26452
chr2	199009458	199009726	E069	26600
chr2	199010610	199010667	E069	27752
chr2	199010781	199010871	E069	27923
chr2	199011098	199011243	E069	28240
chr2	199011257	199011634	E069	28399
chr2	199026677	199026731	E069	43819
chr2	199028379	199028419	E069	45521
chr2	198945273	198945529	E071	-37329
chr2	198960865	198960964	E071	-21894
chr2	198961450	198961502	E071	-21356
chr2	198961841	198961912	E071	-20946
chr2	198962411	198962470	E071	-20388
chr2	198963763	198963935	E071	-18923
chr2	198965149	198965308	E071	-17550
chr2	198975540	198975603	E071	-7255
chr2	198977050	198977114	E071	-5744
chr2	198981402	198981945	E071	-913
chr2	198982067	198982154	E071	-704
chr2	198982183	198982417	E071	-441
chr2	198995651	198995903	E071	12793
chr2	198998950	198999284	E071	16092
chr2	198999297	198999591	E071	16439
chr2	198999803	198999847	E071	16945
chr2	199000215	199000640	E071	17357
chr2	199006417	199006896	E071	23559
chr2	199009310	199009414	E071	26452
chr2	199009458	199009726	E071	26600
chr2	199010610	199010667	E071	27752
chr2	199010781	199010871	E071	27923
chr2	199011098	199011243	E071	28240
chr2	199025910	199026414	E071	43052
chr2	199026493	199026575	E071	43635
chr2	199026677	199026731	E071	43819
chr2	199028379	199028419	E071	45521
chr2	199029683	199029855	E071	46825
chr2	198945273	198945529	E072	-37329
chr2	198961841	198961912	E072	-20946
chr2	198962411	198962470	E072	-20388
chr2	198965149	198965308	E072	-17550
chr2	198975540	198975603	E072	-7255
chr2	198977050	198977114	E072	-5744
chr2	198978077	198978371	E072	-4487
chr2	198989790	198989843	E072	6932
chr2	198989886	198989996	E072	7028
chr2	198998950	198999284	E072	16092
chr2	198999297	198999591	E072	16439
chr2	198999803	198999847	E072	16945
chr2	199006417	199006896	E072	23559
chr2	199009310	199009414	E072	26452
chr2	199009458	199009726	E072	26600
chr2	199010610	199010667	E072	27752
chr2	199010781	199010871	E072	27923
chr2	199011098	199011243	E072	28240
chr2	199028379	199028419	E072	45521
chr2	198962411	198962470	E073	-20388
chr2	198965149	198965308	E073	-17550
chr2	198945273	198945529	E074	-37329
chr2	198961841	198961912	E074	-20946
chr2	198962411	198962470	E074	-20388
chr2	198963763	198963935	E074	-18923
chr2	198965149	198965308	E074	-17550
chr2	198975540	198975603	E074	-7255
chr2	198978077	198978371	E074	-4487
chr2	198978425	198978498	E074	-4360
chr2	198978866	198979373	E074	-3485
chr2	198979410	198979460	E074	-3398
chr2	198979807	198979926	E074	-2932
chr2	198980083	198980143	E074	-2715
chr2	198984220	198984270	E074	1362
chr2	198999297	198999591	E074	16439
chr2	198999803	198999847	E074	16945
chr2	199000215	199000640	E074	17357
chr2	199009310	199009414	E074	26452
chr2	199009458	199009726	E074	26600
chr2	199010610	199010667	E074	27752
chr2	199010781	199010871	E074	27923
chr2	199011098	199011243	E074	28240
chr2	199011257	199011634	E074	28399
chr2	199028379	199028419	E074	45521
chr2	199029683	199029855	E074	46825
chr2	198945273	198945529	E081	-37329
chr2	199031557	199031742	E081	48699
chr2	199032196	199032420	E081	49338
chr2	199032669	199032723	E081	49811
chr2	199032196	199032420	E082	49338
chr2	199032669	199032723	E082	49811