rs4757381

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

MICALCL : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0394 (11645/29542,GnomAD)
A=0338 (9844/29118,TOPMED)
A=0323 (1618/5008,1000G)
A=0471 (1814/3854,ALSPAC)
A=0481 (1785/3708,TWINSUK)

Position: chr11:12347098 (GRCh38.p7) (11p15.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 61 Enhancers around

Promoter: 17 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.12347098G>A
GRCh37.p13 chr 11	NC_000011.9:g.12368645G>A

Gene: MICALCL, MICAL C-terminal like(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MICALCL transcript	NM_032867.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.819	A=0.181
1000Genomes	American	Sub	694	G=0.720	A=0.280
1000Genomes	East Asian	Sub	1008	G=0.622	A=0.378
1000Genomes	Europe	Sub	1006	G=0.529	A=0.471
1000Genomes	Global	Study-wide	5008	G=0.677	A=0.323
1000Genomes	South Asian	Sub	978	G=0.660	A=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.529	A=0.471
The Genome Aggregation Database	African	Sub	8556	G=0.814	A=0.186
The Genome Aggregation Database	American	Sub	826	G=0.710	A=0.290
The Genome Aggregation Database	East Asian	Sub	1594	G=0.666	A=0.334
The Genome Aggregation Database	Europe	Sub	18266	G=0.498	A=0.501
The Genome Aggregation Database	Global	Study-wide	29542	G=0.605	A=0.394
The Genome Aggregation Database	Other	Sub	300	G=0.560	A=0.440
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.661	A=0.338
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.519	A=0.481

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs4757381	0.0000895	alcoholism	pha002891
rs4757381	0.0000895	alcohol dependence	20201924

eQTL of rs4757381 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 rs4757381 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	12346506	12346609	E068	-22036
chr11	12350867	12351060	E068	-17585
chr11	12351478	12351691	E068	-16954
chr11	12411932	12412760	E068	43287
chr11	12346506	12346609	E069	-22036
chr11	12350403	12350457	E069	-18188
chr11	12350867	12351060	E069	-17585
chr11	12351478	12351691	E069	-16954
chr11	12351923	12353236	E069	-15409
chr11	12340278	12340415	E070	-28230
chr11	12340445	12340956	E070	-27689
chr11	12341009	12341274	E070	-27371
chr11	12341326	12341571	E070	-27074
chr11	12350403	12350457	E070	-18188
chr11	12353402	12353477	E070	-15168
chr11	12353535	12353593	E070	-15052
chr11	12340445	12340956	E071	-27689
chr11	12341009	12341274	E071	-27371
chr11	12350403	12350457	E071	-18188
chr11	12350867	12351060	E071	-17585
chr11	12351478	12351691	E071	-16954
chr11	12411139	12411882	E071	42494
chr11	12411932	12412760	E071	43287
chr11	12347341	12347391	E072	-21254
chr11	12351478	12351691	E072	-16954
chr11	12351923	12353236	E072	-15409
chr11	12411932	12412760	E072	43287
chr11	12350867	12351060	E073	-17585
chr11	12351478	12351691	E073	-16954
chr11	12351923	12353236	E073	-15409
chr11	12411139	12411882	E073	42494
chr11	12411932	12412760	E073	43287
chr11	12346506	12346609	E074	-22036
chr11	12350403	12350457	E074	-18188
chr11	12350867	12351060	E074	-17585
chr11	12351478	12351691	E074	-16954
chr11	12351923	12353236	E074	-15409
chr11	12340278	12340415	E081	-28230
chr11	12340445	12340956	E081	-27689
chr11	12341009	12341274	E081	-27371
chr11	12341326	12341571	E081	-27074
chr11	12341968	12342137	E081	-26508
chr11	12342177	12342342	E081	-26303
chr11	12351923	12353236	E081	-15409
chr11	12365070	12365402	E081	-3243
chr11	12366732	12366826	E081	-1819
chr11	12384289	12384364	E081	15644
chr11	12411139	12411882	E081	42494
chr11	12411932	12412760	E081	43287
chr11	12412777	12412884	E081	44132
chr11	12412993	12413053	E081	44348
chr11	12340278	12340415	E082	-28230
chr11	12340445	12340956	E082	-27689
chr11	12341009	12341274	E082	-27371
chr11	12341326	12341571	E082	-27074
chr11	12341968	12342137	E082	-26508
chr11	12342177	12342342	E082	-26303
chr11	12342568	12342613	E082	-26032
chr11	12351478	12351691	E082	-16954
chr11	12411932	12412760	E082	43287
chr11	12412777	12412884	E082	44132

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr11	12397727	12400096	E067	29082
chr11	12400175	12400304	E067	31530
chr11	12397727	12400096	E068	29082
chr11	12400175	12400304	E068	31530
chr11	12397727	12400096	E069	29082
chr11	12397727	12400096	E070	29082
chr11	12400175	12400304	E070	31530
chr11	12397727	12400096	E071	29082
chr11	12400175	12400304	E071	31530
chr11	12397727	12400096	E072	29082
chr11	12400175	12400304	E072	31530
chr11	12397727	12400096	E073	29082
chr11	12400175	12400304	E073	31530
chr11	12397727	12400096	E074	29082
chr11	12400175	12400304	E081	31530
chr11	12397727	12400096	E082	29082
chr11	12400175	12400304	E082	31530