rs10831798

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

MICALCL : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0425 (12734/29912,GnomAD)
C=0382 (11131/29118,TOPMED)
C=0334 (1675/5008,1000G)
C=0495 (1909/3854,ALSPAC)
C=0499 (1851/3708,TWINSUK)

Position: chr11:12346259 (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.12346259T>C
GRCh37.p13 chr 11	NC_000011.9:g.12367806T>C

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

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.758	C=0.242
1000Genomes	American	Sub	694	T=0.710	C=0.290
1000Genomes	East Asian	Sub	1008	T=0.678	C=0.322
1000Genomes	Europe	Sub	1006	T=0.520	C=0.480
1000Genomes	Global	Study-wide	5008	T=0.666	C=0.334
1000Genomes	South Asian	Sub	978	T=0.650	C=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.505	C=0.495
The Genome Aggregation Database	African	Sub	8704	T=0.749	C=0.251
The Genome Aggregation Database	American	Sub	834	T=0.730	C=0.270
The Genome Aggregation Database	East Asian	Sub	1612	T=0.708	C=0.292
The Genome Aggregation Database	Europe	Sub	18460	T=0.473	C=0.526
The Genome Aggregation Database	Global	Study-wide	29912	T=0.574	C=0.425
The Genome Aggregation Database	Other	Sub	302	T=0.560	C=0.440
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.617	C=0.382
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.501	C=0.499

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

SNP ID	p-value	Traits	Study
rs10831798	0.0000278	alcoholism	pha002891
rs10831798	0.0000278	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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	-21197
chr11	12350867	12351060	E068	-16746
chr11	12351478	12351691	E068	-16115
chr11	12411932	12412760	E068	44126
chr11	12346506	12346609	E069	-21197
chr11	12350403	12350457	E069	-17349
chr11	12350867	12351060	E069	-16746
chr11	12351478	12351691	E069	-16115
chr11	12351923	12353236	E069	-14570
chr11	12340278	12340415	E070	-27391
chr11	12340445	12340956	E070	-26850
chr11	12341009	12341274	E070	-26532
chr11	12341326	12341571	E070	-26235
chr11	12350403	12350457	E070	-17349
chr11	12353402	12353477	E070	-14329
chr11	12353535	12353593	E070	-14213
chr11	12340445	12340956	E071	-26850
chr11	12341009	12341274	E071	-26532
chr11	12350403	12350457	E071	-17349
chr11	12350867	12351060	E071	-16746
chr11	12351478	12351691	E071	-16115
chr11	12411139	12411882	E071	43333
chr11	12411932	12412760	E071	44126
chr11	12347341	12347391	E072	-20415
chr11	12351478	12351691	E072	-16115
chr11	12351923	12353236	E072	-14570
chr11	12411932	12412760	E072	44126
chr11	12350867	12351060	E073	-16746
chr11	12351478	12351691	E073	-16115
chr11	12351923	12353236	E073	-14570
chr11	12411139	12411882	E073	43333
chr11	12411932	12412760	E073	44126
chr11	12346506	12346609	E074	-21197
chr11	12350403	12350457	E074	-17349
chr11	12350867	12351060	E074	-16746
chr11	12351478	12351691	E074	-16115
chr11	12351923	12353236	E074	-14570
chr11	12340278	12340415	E081	-27391
chr11	12340445	12340956	E081	-26850
chr11	12341009	12341274	E081	-26532
chr11	12341326	12341571	E081	-26235
chr11	12341968	12342137	E081	-25669
chr11	12342177	12342342	E081	-25464
chr11	12351923	12353236	E081	-14570
chr11	12365070	12365402	E081	-2404
chr11	12366732	12366826	E081	-980
chr11	12384289	12384364	E081	16483
chr11	12411139	12411882	E081	43333
chr11	12411932	12412760	E081	44126
chr11	12412777	12412884	E081	44971
chr11	12412993	12413053	E081	45187
chr11	12340278	12340415	E082	-27391
chr11	12340445	12340956	E082	-26850
chr11	12341009	12341274	E082	-26532
chr11	12341326	12341571	E082	-26235
chr11	12341968	12342137	E082	-25669
chr11	12342177	12342342	E082	-25464
chr11	12342568	12342613	E082	-25193
chr11	12351478	12351691	E082	-16115
chr11	12411932	12412760	E082	44126
chr11	12412777	12412884	E082	44971

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr11	12397727	12400096	E067	29921
chr11	12400175	12400304	E067	32369
chr11	12397727	12400096	E068	29921
chr11	12400175	12400304	E068	32369
chr11	12397727	12400096	E069	29921
chr11	12397727	12400096	E070	29921
chr11	12400175	12400304	E070	32369
chr11	12397727	12400096	E071	29921
chr11	12400175	12400304	E071	32369
chr11	12397727	12400096	E072	29921
chr11	12400175	12400304	E072	32369
chr11	12397727	12400096	E073	29921
chr11	12400175	12400304	E073	32369
chr11	12397727	12400096	E074	29921
chr11	12400175	12400304	E081	32369
chr11	12397727	12400096	E082	29921
chr11	12400175	12400304	E082	32369

rs10831798

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs10831798 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs10831798 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)