rs4883071

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CLEC4A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0145 (4351/29918,GnomAD)
A==0213 (6217/29118,TOPMED)
A==0185 (926/5008,1000G)
A==0013 (51/3854,ALSPAC)
A==0011 (40/3708,TWINSUK)

Position: chr12:8118506 (GRCh38.p7) (12p13.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 89 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.8118506A>G
GRCh37.p13 chr 12	NC_000012.11:g.8271102A>G

Gene: CLEC4A, C-type lectin domain family 4 member A(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLEC4A transcript variant 1	NM_016184.3:c.	N/A	Genic Upstream Transcript Variant
CLEC4A transcript variant 3	NM_194447.2:c.	N/A	Genic Upstream Transcript Variant
CLEC4A transcript variant 4	NM_194448.2:c.	N/A	Genic Upstream Transcript Variant
CLEC4A transcript variant 2	NM_194450.2:c.	N/A	Genic Upstream Transcript Variant
CLEC4A transcript variant X2	XM_017019382.1:c.	N/A	Intron Variant
CLEC4A transcript variant X1	XM_011520684.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.535	G=0.465
1000Genomes	American	Sub	694	A=0.060	G=0.940
1000Genomes	East Asian	Sub	1008	A=0.025	G=0.975
1000Genomes	Europe	Sub	1006	A=0.018	G=0.982
1000Genomes	Global	Study-wide	5008	A=0.185	G=0.815
1000Genomes	South Asian	Sub	978	A=0.140	G=0.860
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.013	G=0.987
The Genome Aggregation Database	African	Sub	8684	A=0.455	G=0.545
The Genome Aggregation Database	American	Sub	838	A=0.040	G=0.960
The Genome Aggregation Database	East Asian	Sub	1622	A=0.030	G=0.970
The Genome Aggregation Database	Europe	Sub	18472	A=0.017	G=0.982
The Genome Aggregation Database	Global	Study-wide	29918	A=0.145	G=0.854
The Genome Aggregation Database	Other	Sub	302	A=0.000	G=1.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.213	G=0.786
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.011	G=0.989

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
rs4883071	9.78E-05	alcohol dependence	21314694

eQTL of rs4883071 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 rs4883071 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg08814206	chr6:32122676	PPT2	0.0294773863593902	4.5800e-9

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 )
chr12	8236053	8236097	E067	-35005
chr12	8236148	8236188	E067	-34914
chr12	8236358	8236440	E067	-34662
chr12	8236602	8236700	E067	-34402
chr12	8236807	8237045	E067	-34057
chr12	8237112	8237376	E067	-33726
chr12	8237420	8237559	E067	-33543
chr12	8237651	8237701	E067	-33401
chr12	8238050	8238177	E067	-32925
chr12	8261319	8261426	E067	-9676
chr12	8232428	8232792	E068	-38310
chr12	8232810	8233010	E068	-38092
chr12	8233026	8233329	E068	-37773
chr12	8233433	8233553	E068	-37549
chr12	8233671	8233733	E068	-37369
chr12	8236053	8236097	E068	-35005
chr12	8236148	8236188	E068	-34914
chr12	8236358	8236440	E068	-34662
chr12	8236602	8236700	E068	-34402
chr12	8236807	8237045	E068	-34057
chr12	8297976	8298026	E068	26874
chr12	8233026	8233329	E069	-37773
chr12	8236053	8236097	E069	-35005
chr12	8236148	8236188	E069	-34914
chr12	8236358	8236440	E069	-34662
chr12	8236602	8236700	E069	-34402
chr12	8236807	8237045	E069	-34057
chr12	8237112	8237376	E069	-33726
chr12	8261319	8261426	E069	-9676
chr12	8261437	8261848	E069	-9254
chr12	8299442	8299492	E069	28340
chr12	8236053	8236097	E070	-35005
chr12	8236148	8236188	E070	-34914
chr12	8236358	8236440	E070	-34662
chr12	8236807	8237045	E070	-34057
chr12	8237112	8237376	E070	-33726
chr12	8297527	8297577	E070	26425
chr12	8297603	8297653	E070	26501
chr12	8297703	8297743	E070	26601
chr12	8298324	8299402	E070	27222
chr12	8232428	8232792	E071	-38310
chr12	8232810	8233010	E071	-38092
chr12	8233026	8233329	E071	-37773
chr12	8233433	8233553	E071	-37549
chr12	8233671	8233733	E071	-37369
chr12	8236053	8236097	E071	-35005
chr12	8236148	8236188	E071	-34914
chr12	8236358	8236440	E071	-34662
chr12	8236602	8236700	E071	-34402
chr12	8236807	8237045	E071	-34057
chr12	8237112	8237376	E071	-33726
chr12	8261319	8261426	E071	-9676
chr12	8261437	8261848	E071	-9254
chr12	8236053	8236097	E072	-35005
chr12	8236148	8236188	E072	-34914
chr12	8236358	8236440	E072	-34662
chr12	8236602	8236700	E072	-34402
chr12	8236807	8237045	E072	-34057
chr12	8237112	8237376	E072	-33726
chr12	8261319	8261426	E072	-9676
chr12	8230899	8231279	E073	-39823
chr12	8231342	8231400	E073	-39702
chr12	8231562	8231656	E073	-39446
chr12	8236053	8236097	E073	-35005
chr12	8236148	8236188	E073	-34914
chr12	8236358	8236440	E073	-34662
chr12	8236602	8236700	E073	-34402
chr12	8236807	8237045	E073	-34057
chr12	8299442	8299492	E073	28340
chr12	8232810	8233010	E074	-38092
chr12	8233026	8233329	E074	-37773
chr12	8233433	8233553	E074	-37549
chr12	8233671	8233733	E074	-37369
chr12	8236053	8236097	E074	-35005
chr12	8236148	8236188	E074	-34914
chr12	8236358	8236440	E074	-34662
chr12	8236602	8236700	E074	-34402
chr12	8236807	8237045	E074	-34057
chr12	8261319	8261426	E074	-9676
chr12	8261437	8261848	E074	-9254
chr12	8261927	8261990	E074	-9112
chr12	8299442	8299492	E074	28340
chr12	8236053	8236097	E081	-35005
chr12	8236148	8236188	E081	-34914
chr12	8236358	8236440	E081	-34662
chr12	8236602	8236700	E081	-34402
chr12	8236807	8237045	E081	-34057
chr12	8237112	8237376	E081	-33726
chr12	8233671	8233733	E082	-37369

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	8233750	8235845	E067	-35257
chr12	8233750	8235845	E068	-35257
chr12	8233750	8235845	E069	-35257
chr12	8233750	8235845	E070	-35257
chr12	8233750	8235845	E071	-35257
chr12	8233750	8235845	E072	-35257
chr12	8233750	8235845	E073	-35257
chr12	8233750	8235845	E074	-35257
chr12	8233750	8235845	E082	-35257