rs7176042

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

GCOM1 : Intron Variant
MYZAP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0279 (8346/29908,GnomAD)
A=0216 (1080/5008,1000G)
A=0339 (1306/3854,ALSPAC)
A=0344 (1274/3708,TWINSUK)

Position: chr15:57642503 (GRCh38.p7) (15q21.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 1 Enhancer around

Promoter: 74 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.57642503G>A
GRCh38.p7 chr 15	NC_000015.10:g.57642503G>T
GRCh37.p13 chr 15	NC_000015.9:g.57934701G>A
GRCh37.p13 chr 15	NC_000015.9:g.57934701G>T

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	G=0.856	A=0.144
1000Genomes	American	Sub	694	G=0.650	A=0.350
1000Genomes	East Asian	Sub	1008	G=0.886	A=0.114
1000Genomes	Europe	Sub	1006	G=0.662	A=0.338
1000Genomes	Global	Study-wide	5008	G=0.784	A=0.216
1000Genomes	South Asian	Sub	978	G=0.800	A=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.661	A=0.339
The Genome Aggregation Database	African	Sub	8714	G=0.832	A=0.168
The Genome Aggregation Database	American	Sub	836	G=0.640	A=0.360
The Genome Aggregation Database	East Asian	Sub	1612	G=0.849	A=0.151
The Genome Aggregation Database	Europe	Sub	18448	G=0.660	A=0.339
The Genome Aggregation Database	Global	Study-wide	29908	G=0.720	A=0.279
The Genome Aggregation Database	Other	Sub	298	G=0.780	A=0.220
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.656	A=0.344

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
rs7176042	0.00061	alcohol dependence	20201924

eQTL of rs7176042 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 rs7176042 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	30936482	30936546	E070	16358

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr15	30916640	30916807	E067	-3317
chr15	30916858	30916920	E067	-3204
chr15	30917167	30917230	E067	-2894
chr15	30917348	30917416	E067	-2708
chr15	30917647	30918139	E067	-1985
chr15	30918149	30918399	E067	-1725
chr15	30918571	30918795	E067	-1329
chr15	30916640	30916807	E068	-3317
chr15	30916858	30916920	E068	-3204
chr15	30917167	30917230	E068	-2894
chr15	30917348	30917416	E068	-2708
chr15	30917647	30918139	E068	-1985
chr15	30918149	30918399	E068	-1725
chr15	30918571	30918795	E068	-1329
chr15	30916640	30916807	E069	-3317
chr15	30916858	30916920	E069	-3204
chr15	30917167	30917230	E069	-2894
chr15	30917348	30917416	E069	-2708
chr15	30917647	30918139	E069	-1985
chr15	30918149	30918399	E069	-1725
chr15	30918571	30918795	E069	-1329
chr15	30916640	30916807	E070	-3317
chr15	30916858	30916920	E070	-3204
chr15	30917167	30917230	E070	-2894
chr15	30917348	30917416	E070	-2708
chr15	30917647	30918139	E070	-1985
chr15	30918149	30918399	E070	-1725
chr15	30918571	30918795	E070	-1329
chr15	30918976	30919079	E070	-1045
chr15	30919257	30919326	E070	-798
chr15	30919486	30919540	E070	-584
chr15	30919861	30919911	E070	-213
chr15	30916640	30916807	E071	-3317
chr15	30916858	30916920	E071	-3204
chr15	30917167	30917230	E071	-2894
chr15	30917348	30917416	E071	-2708
chr15	30917647	30918139	E071	-1985
chr15	30918149	30918399	E071	-1725
chr15	30918571	30918795	E071	-1329
chr15	30916640	30916807	E072	-3317
chr15	30916858	30916920	E072	-3204
chr15	30917167	30917230	E072	-2894
chr15	30917348	30917416	E072	-2708
chr15	30917647	30918139	E072	-1985
chr15	30918149	30918399	E072	-1725
chr15	30918571	30918795	E072	-1329
chr15	30918976	30919079	E072	-1045
chr15	30916858	30916920	E073	-3204
chr15	30917167	30917230	E073	-2894
chr15	30917348	30917416	E073	-2708
chr15	30917647	30918139	E073	-1985
chr15	30918149	30918399	E073	-1725
chr15	30918571	30918795	E073	-1329
chr15	30916858	30916920	E074	-3204
chr15	30917647	30918139	E074	-1985
chr15	30918149	30918399	E074	-1725
chr15	30918571	30918795	E074	-1329
chr15	30916640	30916807	E081	-3317
chr15	30916858	30916920	E081	-3204
chr15	30917167	30917230	E081	-2894
chr15	30917348	30917416	E081	-2708
chr15	30917647	30918139	E081	-1985
chr15	30918149	30918399	E081	-1725
chr15	30918571	30918795	E081	-1329
chr15	30916640	30916807	E082	-3317
chr15	30916858	30916920	E082	-3204
chr15	30917167	30917230	E082	-2894
chr15	30917348	30917416	E082	-2708
chr15	30917647	30918139	E082	-1985
chr15	30918149	30918399	E082	-1725
chr15	30918571	30918795	E082	-1329
chr15	30918976	30919079	E082	-1045
chr15	30919257	30919326	E082	-798
chr15	30919486	30919540	E082	-584