rs4369393

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

LRRC4C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0473 (14145/29882,GnomAD)
T=0432 (12595/29118,TOPMED)
T=0474 (2375/5008,1000G)
G==0481 (1854/3854,ALSPAC)
G==0476 (1764/3708,TWINSUK)

Position: chr11:40204831 (GRCh38.p7) (11p12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 301 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.40204831G>T
GRCh37.p13 chr 11	NC_000011.9:g.40226381G>T

Gene: LRRC4C, leucine rich repeat containing 4C(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRRC4C transcript variant 2	NM_001258419.1:c.	N/A	Intron Variant
LRRC4C transcript variant 1	NM_020929.2:c.	N/A	Intron Variant
LRRC4C transcript variant 3	NR_047673.1:n.	N/A	Intron Variant
LRRC4C transcript variant 4	NR_047674.1:n.	N/A	Intron Variant
LRRC4C transcript variant X1	XM_011520238.2:c.	N/A	Intron Variant
LRRC4C transcript variant X2	XM_011520239.2:c.	N/A	Intron Variant
LRRC4C transcript variant X3	XM_011520240.2:c.	N/A	Intron Variant
LRRC4C transcript variant X9	XM_011520241.2:c.	N/A	Intron Variant
LRRC4C transcript variant X11	XM_011520242.2:c.	N/A	Intron Variant
LRRC4C transcript variant X8	XM_011520243.2:c.	N/A	Intron Variant
LRRC4C transcript variant X10	XM_011520244.2:c.	N/A	Intron Variant
LRRC4C transcript variant X4	XM_017018070.1:c.	N/A	Intron Variant
LRRC4C transcript variant X5	XM_017018071.1:c.	N/A	Intron Variant
LRRC4C transcript variant X6	XM_017018072.1:c.	N/A	Intron Variant
LRRC4C transcript variant X7	XM_017018073.1:c.	N/A	Intron Variant
LRRC4C transcript variant X12	XM_017018074.1:c.	N/A	Intron Variant
LRRC4C transcript variant X13	XM_017018075.1:c.	N/A	Intron Variant
LRRC4C transcript variant X14	XM_017018076.1:c.	N/A	Intron Variant
LRRC4C transcript variant X15	XM_017018077.1:c.	N/A	Intron Variant
LRRC4C transcript variant X16	XM_017018078.1:c.	N/A	Intron Variant
LRRC4C transcript variant X17	XM_017018079.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.764	T=0.236
1000Genomes	American	Sub	694	G=0.420	T=0.580
1000Genomes	East Asian	Sub	1008	G=0.366	T=0.634
1000Genomes	Europe	Sub	1006	G=0.471	T=0.529
1000Genomes	Global	Study-wide	5008	G=0.526	T=0.474
1000Genomes	South Asian	Sub	978	G=0.500	T=0.500
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.481	T=0.519
The Genome Aggregation Database	African	Sub	8692	G=0.717	T=0.283
The Genome Aggregation Database	American	Sub	834	G=0.410	T=0.590
The Genome Aggregation Database	East Asian	Sub	1606	G=0.391	T=0.609
The Genome Aggregation Database	Europe	Sub	18448	G=0.455	T=0.544
The Genome Aggregation Database	Global	Study-wide	29882	G=0.526	T=0.473
The Genome Aggregation Database	Other	Sub	302	G=0.450	T=0.550
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.567	T=0.432
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.476	T=0.524

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

P-Value

SNP ID	p-value	Traits	Study
rs4369393	0.000937	alcohol dependence	21314694

eQTL of rs4369393 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 rs4369393 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 )
chr11	40183664	40183853	E067	-42528
chr11	40189995	40190330	E067	-36051
chr11	40190342	40190392	E067	-35989
chr11	40196565	40196605	E067	-29776
chr11	40196609	40196783	E067	-29598
chr11	40196836	40197125	E067	-29256
chr11	40197138	40197225	E067	-29156
chr11	40201978	40202072	E067	-24309
chr11	40202221	40202319	E067	-24062
chr11	40203139	40203257	E067	-23124
chr11	40203382	40203423	E067	-22958
chr11	40204788	40204918	E067	-21463
chr11	40205025	40205157	E067	-21224
chr11	40205179	40205239	E067	-21142
chr11	40205278	40205328	E067	-21053
chr11	40205351	40205408	E067	-20973
chr11	40205606	40205680	E067	-20701
chr11	40206268	40206340	E067	-20041
chr11	40208666	40208855	E067	-17526
chr11	40209098	40209184	E067	-17197
chr11	40209366	40209491	E067	-16890
chr11	40209656	40209710	E067	-16671
chr11	40209854	40209921	E067	-16460
chr11	40210388	40210438	E067	-15943
chr11	40210521	40210665	E067	-15716
chr11	40211085	40211135	E067	-15246
chr11	40211249	40211309	E067	-15072
chr11	40222594	40222644	E067	-3737
chr11	40222725	40222779	E067	-3602
chr11	40223160	40223281	E067	-3100
chr11	40223468	40223547	E067	-2834
chr11	40223703	40223753	E067	-2628
chr11	40223887	40223927	E067	-2454
chr11	40224090	40224449	E067	-1932
chr11	40224538	40224734	E067	-1647
chr11	40225011	40225136	E067	-1245
chr11	40225198	40225423	E067	-958
chr11	40230416	40230515	E067	4035
chr11	40247758	40247816	E067	21377
chr11	40247957	40248007	E067	21576
chr11	40248340	40248518	E067	21959
chr11	40250082	40250212	E067	23701
chr11	40250342	40250547	E067	23961
chr11	40251152	40251202	E067	24771
chr11	40251295	40251444	E067	24914
chr11	40252539	40252677	E067	26158
chr11	40273173	40273223	E067	46792
chr11	40275773	40275827	E067	49392
chr11	40180902	40180967	E068	-45414
chr11	40183664	40183853	E068	-42528
chr11	40184008	40184089	E068	-42292
chr11	40184308	40184579	E068	-41802
chr11	40196836	40197125	E068	-29256
chr11	40197138	40197225	E068	-29156
chr11	40197296	40197349	E068	-29032
chr11	40201978	40202072	E068	-24309
chr11	40202221	40202319	E068	-24062
chr11	40203139	40203257	E068	-23124
chr11	40203382	40203423	E068	-22958
chr11	40203876	40203926	E068	-22455
chr11	40206268	40206340	E068	-20041
chr11	40206925	40207038	E068	-19343
chr11	40207430	40207518	E068	-18863
chr11	40209098	40209184	E068	-17197
chr11	40209366	40209491	E068	-16890
chr11	40209656	40209710	E068	-16671
chr11	40209854	40209921	E068	-16460
chr11	40210388	40210438	E068	-15943
chr11	40210521	40210665	E068	-15716
chr11	40211085	40211135	E068	-15246
chr11	40211249	40211309	E068	-15072
chr11	40222594	40222644	E068	-3737
chr11	40223160	40223281	E068	-3100
chr11	40223468	40223547	E068	-2834
chr11	40223703	40223753	E068	-2628
chr11	40223887	40223927	E068	-2454
chr11	40224090	40224449	E068	-1932
chr11	40237171	40237355	E068	10790
chr11	40247662	40247702	E068	21281
chr11	40247758	40247816	E068	21377
chr11	40247957	40248007	E068	21576
chr11	40249494	40249554	E068	23113
chr11	40249688	40249751	E068	23307
chr11	40249761	40249849	E068	23380
chr11	40250082	40250212	E068	23701
chr11	40250342	40250547	E068	23961
chr11	40252539	40252677	E068	26158
chr11	40257962	40258039	E068	31581
chr11	40273173	40273223	E068	46792
chr11	40273690	40273740	E068	47309
chr11	40183664	40183853	E069	-42528
chr11	40184008	40184089	E069	-42292
chr11	40189995	40190330	E069	-36051
chr11	40190342	40190392	E069	-35989
chr11	40191784	40191852	E069	-34529
chr11	40191857	40191915	E069	-34466
chr11	40203139	40203257	E069	-23124
chr11	40203382	40203423	E069	-22958
chr11	40203876	40203926	E069	-22455
chr11	40204788	40204918	E069	-21463
chr11	40205025	40205157	E069	-21224
chr11	40205179	40205239	E069	-21142
chr11	40205278	40205328	E069	-21053
chr11	40205351	40205408	E069	-20973
chr11	40205606	40205680	E069	-20701
chr11	40206268	40206340	E069	-20041
chr11	40206925	40207038	E069	-19343
chr11	40207430	40207518	E069	-18863
chr11	40208666	40208855	E069	-17526
chr11	40209098	40209184	E069	-17197
chr11	40209366	40209491	E069	-16890
chr11	40209656	40209710	E069	-16671
chr11	40209854	40209921	E069	-16460
chr11	40210388	40210438	E069	-15943
chr11	40210521	40210665	E069	-15716
chr11	40211085	40211135	E069	-15246
chr11	40211249	40211309	E069	-15072
chr11	40222594	40222644	E069	-3737
chr11	40222725	40222779	E069	-3602
chr11	40223160	40223281	E069	-3100
chr11	40223468	40223547	E069	-2834
chr11	40223703	40223753	E069	-2628
chr11	40223887	40223927	E069	-2454
chr11	40224090	40224449	E069	-1932
chr11	40224538	40224734	E069	-1647
chr11	40225011	40225136	E069	-1245
chr11	40225198	40225423	E069	-958
chr11	40237171	40237355	E069	10790
chr11	40252539	40252677	E069	26158
chr11	40263052	40263724	E069	36671
chr11	40274852	40275007	E069	48471
chr11	40275773	40275827	E069	49392
chr11	40208666	40208855	E070	-17526
chr11	40209098	40209184	E070	-17197
chr11	40189995	40190330	E071	-36051
chr11	40190342	40190392	E071	-35989
chr11	40196414	40196464	E071	-29917
chr11	40196565	40196605	E071	-29776
chr11	40196609	40196783	E071	-29598
chr11	40196836	40197125	E071	-29256
chr11	40197138	40197225	E071	-29156
chr11	40199608	40199652	E071	-26729
chr11	40203139	40203257	E071	-23124
chr11	40203382	40203423	E071	-22958
chr11	40203876	40203926	E071	-22455
chr11	40204533	40204585	E071	-21796
chr11	40204788	40204918	E071	-21463
chr11	40205025	40205157	E071	-21224
chr11	40205179	40205239	E071	-21142
chr11	40205278	40205328	E071	-21053
chr11	40205351	40205408	E071	-20973
chr11	40205606	40205680	E071	-20701
chr11	40206268	40206340	E071	-20041
chr11	40206925	40207038	E071	-19343
chr11	40207430	40207518	E071	-18863
chr11	40208666	40208855	E071	-17526
chr11	40209098	40209184	E071	-17197
chr11	40209366	40209491	E071	-16890
chr11	40209656	40209710	E071	-16671
chr11	40209854	40209921	E071	-16460
chr11	40210388	40210438	E071	-15943
chr11	40210521	40210665	E071	-15716
chr11	40211085	40211135	E071	-15246
chr11	40211249	40211309	E071	-15072
chr11	40223468	40223547	E071	-2834
chr11	40223703	40223753	E071	-2628
chr11	40223887	40223927	E071	-2454
chr11	40224090	40224449	E071	-1932
chr11	40224538	40224734	E071	-1647
chr11	40225011	40225136	E071	-1245
chr11	40237171	40237355	E071	10790
chr11	40247758	40247816	E071	21377
chr11	40247957	40248007	E071	21576
chr11	40248340	40248518	E071	21959
chr11	40248675	40248798	E071	22294
chr11	40249494	40249554	E071	23113
chr11	40249688	40249751	E071	23307
chr11	40249761	40249849	E071	23380
chr11	40250082	40250212	E071	23701
chr11	40250342	40250547	E071	23961
chr11	40252539	40252677	E071	26158
chr11	40275773	40275827	E071	49392
chr11	40189995	40190330	E072	-36051
chr11	40190342	40190392	E072	-35989
chr11	40203139	40203257	E072	-23124
chr11	40203382	40203423	E072	-22958
chr11	40205025	40205157	E072	-21224
chr11	40205179	40205239	E072	-21142
chr11	40205278	40205328	E072	-21053
chr11	40205351	40205408	E072	-20973
chr11	40206268	40206340	E072	-20041
chr11	40206925	40207038	E072	-19343
chr11	40208666	40208855	E072	-17526
chr11	40209098	40209184	E072	-17197
chr11	40209366	40209491	E072	-16890
chr11	40209656	40209710	E072	-16671
chr11	40209854	40209921	E072	-16460
chr11	40210388	40210438	E072	-15943
chr11	40210521	40210665	E072	-15716
chr11	40211085	40211135	E072	-15246
chr11	40211249	40211309	E072	-15072
chr11	40222594	40222644	E072	-3737
chr11	40223160	40223281	E072	-3100
chr11	40223468	40223547	E072	-2834
chr11	40223703	40223753	E072	-2628
chr11	40223887	40223927	E072	-2454
chr11	40224090	40224449	E072	-1932
chr11	40224538	40224734	E072	-1647
chr11	40225011	40225136	E072	-1245
chr11	40247957	40248007	E072	21576
chr11	40249494	40249554	E072	23113
chr11	40249688	40249751	E072	23307
chr11	40249761	40249849	E072	23380
chr11	40250082	40250212	E072	23701
chr11	40250342	40250547	E072	23961
chr11	40252539	40252677	E072	26158
chr11	40273173	40273223	E072	46792
chr11	40273690	40273740	E072	47309
chr11	40273929	40274015	E072	47548
chr11	40189995	40190330	E073	-36051
chr11	40203139	40203257	E073	-23124
chr11	40208666	40208855	E073	-17526
chr11	40209098	40209184	E073	-17197
chr11	40209366	40209491	E073	-16890
chr11	40209656	40209710	E073	-16671
chr11	40210388	40210438	E073	-15943
chr11	40222594	40222644	E073	-3737
chr11	40222725	40222779	E073	-3602
chr11	40223160	40223281	E073	-3100
chr11	40223468	40223547	E073	-2834
chr11	40224090	40224449	E073	-1932
chr11	40224538	40224734	E073	-1647
chr11	40225011	40225136	E073	-1245
chr11	40237171	40237355	E073	10790
chr11	40249494	40249554	E073	23113
chr11	40249688	40249751	E073	23307
chr11	40249761	40249849	E073	23380
chr11	40250082	40250212	E073	23701
chr11	40250342	40250547	E073	23961
chr11	40183664	40183853	E074	-42528
chr11	40184008	40184089	E074	-42292
chr11	40184308	40184579	E074	-41802
chr11	40184591	40184721	E074	-41660
chr11	40197296	40197349	E074	-29032
chr11	40201978	40202072	E074	-24309
chr11	40202221	40202319	E074	-24062
chr11	40203139	40203257	E074	-23124
chr11	40203382	40203423	E074	-22958
chr11	40204533	40204585	E074	-21796
chr11	40204788	40204918	E074	-21463
chr11	40205025	40205157	E074	-21224
chr11	40205179	40205239	E074	-21142
chr11	40205278	40205328	E074	-21053
chr11	40205351	40205408	E074	-20973
chr11	40205606	40205680	E074	-20701
chr11	40206268	40206340	E074	-20041
chr11	40206925	40207038	E074	-19343
chr11	40209098	40209184	E074	-17197
chr11	40209366	40209491	E074	-16890
chr11	40209656	40209710	E074	-16671
chr11	40209854	40209921	E074	-16460
chr11	40210388	40210438	E074	-15943
chr11	40210521	40210665	E074	-15716
chr11	40211085	40211135	E074	-15246
chr11	40211249	40211309	E074	-15072
chr11	40222594	40222644	E074	-3737
chr11	40223160	40223281	E074	-3100
chr11	40223468	40223547	E074	-2834
chr11	40223703	40223753	E074	-2628
chr11	40223887	40223927	E074	-2454
chr11	40224090	40224449	E074	-1932
chr11	40224538	40224734	E074	-1647
chr11	40225011	40225136	E074	-1245
chr11	40225198	40225423	E074	-958
chr11	40225683	40226310	E074	-71
chr11	40247758	40247816	E074	21377
chr11	40247957	40248007	E074	21576
chr11	40248340	40248518	E074	21959
chr11	40248675	40248798	E074	22294
chr11	40249494	40249554	E074	23113
chr11	40249688	40249751	E074	23307
chr11	40249761	40249849	E074	23380
chr11	40250082	40250212	E074	23701
chr11	40250342	40250547	E074	23961
chr11	40257470	40257625	E074	31089
chr11	40257962	40258039	E074	31581
chr11	40263052	40263724	E074	36671
chr11	40275773	40275827	E074	49392
chr11	40222594	40222644	E082	-3737
chr11	40222725	40222779	E082	-3602
chr11	40223160	40223281	E082	-3100
chr11	40223468	40223547	E082	-2834
chr11	40223703	40223753	E082	-2628
chr11	40223887	40223927	E082	-2454
chr11	40224090	40224449	E082	-1932
chr11	40224538	40224734	E082	-1647
chr11	40248675	40248798	E082	22294
chr11	40249761	40249849	E082	23380
chr11	40250082	40250212	E082	23701
chr11	40250342	40250547	E082	23961
chr11	40252539	40252677	E082	26158