rs11801229

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LRRN2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0201 (6038/29932,GnomAD)
G=0236 (6877/29118,TOPMED)
G=0281 (1408/5008,1000G)
G=0147 (568/3854,ALSPAC)
G=0138 (511/3708,TWINSUK)

Position: chr1:204645347 (GRCh38.p7) (1q32.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 119 Enhancers around

Promoter: 26 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.204645347A>G
GRCh37.p13 chr 1	NC_000001.10:g.204614475A>G

Gene: LRRN2, leucine rich repeat neuronal 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRRN2 transcript variant 1	NM_006338.2:c.	N/A	Intron Variant
LRRN2 transcript variant 2	NM_201630.1:c.	N/A	Intron Variant
LRRN2 transcript variant X1	XM_005244827.3:c.	N/A	Intron Variant
LRRN2 transcript variant X3	XM_017000050.1:c.	N/A	Intron Variant
LRRN2 transcript variant X2	XM_011509066.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.688	G=0.312
1000Genomes	American	Sub	694	A=0.860	G=0.140
1000Genomes	East Asian	Sub	1008	A=0.584	G=0.416
1000Genomes	Europe	Sub	1006	A=0.851	G=0.149
1000Genomes	Global	Study-wide	5008	A=0.719	G=0.281
1000Genomes	South Asian	Sub	978	A=0.660	G=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.853	G=0.147
The Genome Aggregation Database	African	Sub	8710	A=0.700	G=0.300
The Genome Aggregation Database	American	Sub	838	A=0.870	G=0.130
The Genome Aggregation Database	East Asian	Sub	1614	A=0.542	G=0.458
The Genome Aggregation Database	Europe	Sub	18468	A=0.864	G=0.135
The Genome Aggregation Database	Global	Study-wide	29932	A=0.798	G=0.201
The Genome Aggregation Database	Other	Sub	302	A=0.760	G=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.763	G=0.236
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.862	G=0.138

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
rs11801229	0.000528	alcohol dependence	21314694

eQTL of rs11801229 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 rs11801229 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 )
chr1	204587128	204587315	E067	-27160
chr1	204639384	204639670	E067	24909
chr1	204639714	204640015	E067	25239
chr1	204642888	204642963	E067	28413
chr1	204643096	204643314	E067	28621
chr1	204643454	204643618	E067	28979
chr1	204643853	204643904	E067	29378
chr1	204586858	204586929	E068	-27546
chr1	204587128	204587315	E068	-27160
chr1	204590409	204590467	E068	-24008
chr1	204590515	204590910	E068	-23565
chr1	204591576	204591718	E068	-22757
chr1	204592490	204592765	E068	-21710
chr1	204592794	204592933	E068	-21542
chr1	204593051	204593108	E068	-21367
chr1	204593125	204593499	E068	-20976
chr1	204593750	204593800	E068	-20675
chr1	204594045	204594345	E068	-20130
chr1	204594571	204594625	E068	-19850
chr1	204602660	204602714	E068	-11761
chr1	204606530	204607469	E068	-7006
chr1	204613994	204614048	E068	-427
chr1	204616716	204616989	E068	2241
chr1	204620041	204620519	E068	5566
chr1	204620754	204621531	E068	6279
chr1	204621849	204621980	E068	7374
chr1	204628241	204628521	E068	13766
chr1	204633317	204633428	E068	18842
chr1	204639384	204639670	E068	24909
chr1	204648306	204648348	E068	33831
chr1	204649714	204649897	E068	35239
chr1	204655799	204655849	E068	41324
chr1	204585954	204586034	E069	-28441
chr1	204586858	204586929	E069	-27546
chr1	204587128	204587315	E069	-27160
chr1	204593125	204593499	E069	-20976
chr1	204593750	204593800	E069	-20675
chr1	204606530	204607469	E069	-7006
chr1	204609874	204609951	E069	-4524
chr1	204616716	204616989	E069	2241
chr1	204633317	204633428	E069	18842
chr1	204642888	204642963	E069	28413
chr1	204643096	204643314	E069	28621
chr1	204643454	204643618	E069	28979
chr1	204643853	204643904	E069	29378
chr1	204586858	204586929	E070	-27546
chr1	204587128	204587315	E070	-27160
chr1	204593125	204593499	E070	-20976
chr1	204593750	204593800	E070	-20675
chr1	204594045	204594345	E070	-20130
chr1	204599609	204599762	E070	-14713
chr1	204606530	204607469	E070	-7006
chr1	204621849	204621980	E070	7374
chr1	204628241	204628521	E070	13766
chr1	204629695	204630003	E070	15220
chr1	204633317	204633428	E070	18842
chr1	204642888	204642963	E070	28413
chr1	204643096	204643314	E070	28621
chr1	204643454	204643618	E070	28979
chr1	204643853	204643904	E070	29378
chr1	204571221	204571626	E071	-42849
chr1	204586858	204586929	E071	-27546
chr1	204587128	204587315	E071	-27160
chr1	204606530	204607469	E071	-7006
chr1	204616396	204616662	E071	1921
chr1	204616716	204616989	E071	2241
chr1	204633317	204633428	E071	18842
chr1	204586858	204586929	E072	-27546
chr1	204616396	204616662	E072	1921
chr1	204616716	204616989	E072	2241
chr1	204629695	204630003	E072	15220
chr1	204633317	204633428	E072	18842
chr1	204642888	204642963	E072	28413
chr1	204643096	204643314	E072	28621
chr1	204643454	204643618	E072	28979
chr1	204643853	204643904	E072	29378
chr1	204647123	204647240	E072	32648
chr1	204648306	204648348	E072	33831
chr1	204580131	204580221	E073	-34254
chr1	204580343	204580443	E073	-34032
chr1	204590409	204590467	E073	-24008
chr1	204590515	204590910	E073	-23565
chr1	204593051	204593108	E073	-21367
chr1	204593125	204593499	E073	-20976
chr1	204593750	204593800	E073	-20675
chr1	204633317	204633428	E073	18842
chr1	204639384	204639670	E073	24909
chr1	204639714	204640015	E073	25239
chr1	204642888	204642963	E073	28413
chr1	204643096	204643314	E073	28621
chr1	204643454	204643618	E073	28979
chr1	204643853	204643904	E073	29378
chr1	204647123	204647240	E073	32648
chr1	204648306	204648348	E073	33831
chr1	204590409	204590467	E074	-24008
chr1	204587128	204587315	E081	-27160
chr1	204591576	204591718	E081	-22757
chr1	204606530	204607469	E081	-7006
chr1	204620041	204620519	E081	5566
chr1	204620754	204621531	E081	6279
chr1	204621849	204621980	E081	7374
chr1	204641622	204642087	E081	27147
chr1	204642888	204642963	E081	28413
chr1	204643096	204643314	E081	28621
chr1	204643454	204643618	E081	28979
chr1	204643853	204643904	E081	29378
chr1	204585954	204586034	E082	-28441
chr1	204586858	204586929	E082	-27546
chr1	204606530	204607469	E082	-7006
chr1	204616716	204616989	E082	2241
chr1	204620041	204620519	E082	5566
chr1	204620754	204621531	E082	6279
chr1	204621849	204621980	E082	7374
chr1	204639714	204640015	E082	25239
chr1	204641622	204642087	E082	27147
chr1	204642888	204642963	E082	28413
chr1	204643096	204643314	E082	28621
chr1	204643454	204643618	E082	28979
chr1	204643853	204643904	E082	29378

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	204652944	204652994	E067	38469
chr1	204653377	204654330	E067	38902
chr1	204654451	204655200	E067	39976
chr1	204652944	204652994	E068	38469
chr1	204653377	204654330	E068	38902
chr1	204654451	204655200	E068	39976
chr1	204652944	204652994	E069	38469
chr1	204653377	204654330	E069	38902
chr1	204654451	204655200	E069	39976
chr1	204652944	204652994	E070	38469
chr1	204654451	204655200	E070	39976
chr1	204652944	204652994	E071	38469
chr1	204653377	204654330	E071	38902
chr1	204654451	204655200	E071	39976
chr1	204652944	204652994	E072	38469
chr1	204653377	204654330	E072	38902
chr1	204654451	204655200	E072	39976
chr1	204652944	204652994	E073	38469
chr1	204653377	204654330	E073	38902
chr1	204654451	204655200	E073	39976
chr1	204652944	204652994	E074	38469
chr1	204653377	204654330	E074	38902
chr1	204654451	204655200	E074	39976
chr1	204652944	204652994	E082	38469
chr1	204653377	204654330	E082	38902
chr1	204654451	204655200	E082	39976