rs1425948

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

GCOM1 : Intron Variant
MYZAP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0324 (9699/29902,GnomAD)
A==0278 (1394/5008,1000G)
A==0356 (1372/3854,ALSPAC)
A==0359 (1333/3708,TWINSUK)

Position: chr15:57665116 (GRCh38.p7) (15q21.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 58 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.57665116A>G
GRCh37.p13 chr 15	NC_000015.9:g.57957314A>G

Gene: GCOM1, GRINL1A complex locus 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GCOM1 transcript variant 1	NM_001018090.6:c.	N/A	Intron Variant
GCOM1 transcript variant 2	NM_001018091.6:c.	N/A	Intron Variant
GCOM1 transcript variant 14	NM_001285900.3:c.	N/A	Intron Variant
GCOM1 transcript variant 10	NR_104367.2:n.	N/A	Intron Variant
GCOM1 transcript variant 3	NR_104368.2:n.	N/A	Intron Variant
GCOM1 transcript variant 4	NR_104369.2:n.	N/A	Intron Variant
GCOM1 transcript variant 5	NR_104370.2:n.	N/A	Intron Variant
GCOM1 transcript variant 9	NR_104371.3:n.	N/A	Intron Variant

Gene: MYZAP, myocardial zonula adherens protein(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MYZAP transcript variant 1	NM_001018100.4:c.	N/A	Intron Variant
MYZAP transcript variant 2	NM_152451.7:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.271	G=0.729
1000Genomes	American	Sub	694	A=0.390	G=0.610
1000Genomes	East Asian	Sub	1008	A=0.131	G=0.869
1000Genomes	Europe	Sub	1006	A=0.354	G=0.646
1000Genomes	Global	Study-wide	5008	A=0.278	G=0.722
1000Genomes	South Asian	Sub	978	A=0.280	G=0.720
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.356	G=0.644
The Genome Aggregation Database	African	Sub	8696	A=0.285	G=0.715
The Genome Aggregation Database	American	Sub	836	A=0.380	G=0.620
The Genome Aggregation Database	East Asian	Sub	1610	A=0.133	G=0.867
The Genome Aggregation Database	Europe	Sub	18458	A=0.358	G=0.641
The Genome Aggregation Database	Global	Study-wide	29902	A=0.324	G=0.675
The Genome Aggregation Database	Other	Sub	302	A=0.240	G=0.760
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.359	G=0.641

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
rs1425948	0.00088	alcohol dependence	20201924

eQTL of rs1425948 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 rs1425948 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 )
chr15	57918995	57919271	E067	-38043
chr15	57977573	57978382	E067	20259
chr15	58000653	58000707	E067	43339
chr15	58000712	58000777	E067	43398
chr15	58000998	58001115	E067	43684
chr15	57918995	57919271	E068	-38043
chr15	57933012	57933062	E069	-24252
chr15	57933094	57933165	E069	-24149
chr15	57943597	57944076	E069	-13238
chr15	57944257	57944318	E069	-12996
chr15	58000653	58000707	E069	43339
chr15	58000712	58000777	E069	43398
chr15	58000998	58001115	E069	43684
chr15	58001281	58001390	E069	43967
chr15	58001508	58001558	E069	44194
chr15	58001666	58001729	E069	44352
chr15	57918657	57918798	E070	-38516
chr15	57918995	57919271	E070	-38043
chr15	57927401	57927490	E070	-29824
chr15	57927572	57928252	E070	-29062
chr15	58000653	58000707	E070	43339
chr15	58000712	58000777	E070	43398
chr15	57945877	57945927	E071	-11387
chr15	58000653	58000707	E071	43339
chr15	58000712	58000777	E071	43398
chr15	58001508	58001558	E071	44194
chr15	58001666	58001729	E071	44352
chr15	58001805	58001849	E071	44491
chr15	58001866	58001939	E071	44552
chr15	57943597	57944076	E072	-13238
chr15	57944257	57944318	E072	-12996
chr15	57945210	57945307	E072	-12007
chr15	58000653	58000707	E072	43339
chr15	58000712	58000777	E072	43398
chr15	58001666	58001729	E072	44352
chr15	58001805	58001849	E072	44491
chr15	58001866	58001939	E072	44552
chr15	58001508	58001558	E073	44194
chr15	58001666	58001729	E073	44352
chr15	57911962	57912302	E074	-45012
chr15	57912327	57912407	E074	-44907
chr15	57918995	57919271	E074	-38043
chr15	57934325	57934412	E074	-22902
chr15	57934486	57934545	E074	-22769
chr15	57927572	57928252	E081	-29062
chr15	58001508	58001558	E081	44194
chr15	57927165	57927209	E082	-30105
chr15	57927256	57927365	E082	-29949
chr15	57927401	57927490	E082	-29824
chr15	57927572	57928252	E082	-29062
chr15	57928468	57928518	E082	-28796
chr15	57928744	57928794	E082	-28520
chr15	58001508	58001558	E082	44194
chr15	58001666	58001729	E082	44352
chr15	58001805	58001849	E082	44491
chr15	58001866	58001939	E082	44552
chr15	58002074	58002128	E082	44760
chr15	58002991	58003072	E082	45677

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr15	57998086	58000532	E067	40772
chr15	57998086	58000532	E068	40772
chr15	57998086	58000532	E069	40772
chr15	57998086	58000532	E070	40772
chr15	57998086	58000532	E071	40772
chr15	57998086	58000532	E072	40772
chr15	57998086	58000532	E073	40772
chr15	57998086	58000532	E074	40772
chr15	57998086	58000532	E081	40772
chr15	57998086	58000532	E082	40772