SNP Detail Info-rs1389733

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.14791717G>T
GRCh37.p13 chr 9	NC_000009.11:g.14791715G>T
FREM1 RefSeqGene	NG_017005.2:g.123520C>A

Gene: FREM1, FRAS1 related extracellular matrix 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FREM1 transcript variant 1	NM_144966.5:c.	N/A	Intron Variant
FREM1 transcript variant 2	NM_001177704.1:c.	N/A	Genic Upstream Transcript Variant
FREM1 transcript variant X9	XM_005251382.3:c.	N/A	Intron Variant
FREM1 transcript variant X22	XM_005251384.4:c.	N/A	Intron Variant
FREM1 transcript variant X21	XM_006716729.3:c.	N/A	Intron Variant
FREM1 transcript variant X1	XM_017014316.1:c.	N/A	Intron Variant
FREM1 transcript variant X2	XM_017014317.1:c.	N/A	Intron Variant
FREM1 transcript variant X3	XM_017014318.1:c.	N/A	Intron Variant
FREM1 transcript variant X4	XM_017014319.1:c.	N/A	Intron Variant
FREM1 transcript variant X5	XM_017014320.1:c.	N/A	Intron Variant
FREM1 transcript variant X6	XM_017014321.1:c.	N/A	Intron Variant
FREM1 transcript variant X6	XM_017014322.1:c.	N/A	Intron Variant
FREM1 transcript variant X7	XM_017014323.1:c.	N/A	Intron Variant
FREM1 transcript variant X10	XM_017014324.1:c.	N/A	Intron Variant
FREM1 transcript variant X11	XM_017014325.1:c.	N/A	Intron Variant
FREM1 transcript variant X11	XM_017014326.1:c.	N/A	Intron Variant
FREM1 transcript variant X13	XM_017014327.1:c.	N/A	Intron Variant
FREM1 transcript variant X14	XM_017014328.1:c.	N/A	Intron Variant
FREM1 transcript variant X15	XM_017014329.1:c.	N/A	Intron Variant
FREM1 transcript variant X20	XM_017014330.1:c.	N/A	Intron Variant
FREM1 transcript variant X20	XM_011517758.2:c.	N/A	Genic Upstream Transcript Variant
FREM1 transcript variant X16	XR_001746194.1:n.	N/A	Intron Variant
FREM1 transcript variant X17	XR_001746195.1:n.	N/A	Intron Variant
FREM1 transcript variant X18	XR_001746196.1:n.	N/A	Intron Variant
FREM1 transcript variant X19	XR_001746197.1:n.	N/A	Intron Variant

Gene: LOC105375979, uncharacterized LOC105375979(plus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105375979 transcript	XR_001746623.1:n.	N/A	Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.666	T=0.334
1000Genomes	American	Sub	694	G=0.450	T=0.550
1000Genomes	East Asian	Sub	1008	G=0.469	T=0.531
1000Genomes	Europe	Sub	1006	G=0.416	T=0.584
1000Genomes	Global	Study-wide	5008	G=0.522	T=0.478
1000Genomes	South Asian	Sub	978	G=0.540	T=0.460
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.418	T=0.582
The Genome Aggregation Database	African	Sub	8708	G=0.623	T=0.377
The Genome Aggregation Database	American	Sub	836	G=0.430	T=0.570
The Genome Aggregation Database	East Asian	Sub	1612	G=0.466	T=0.534
The Genome Aggregation Database	Europe	Sub	18472	G=0.475	T=0.524
The Genome Aggregation Database	Global	Study-wide	29930	G=0.516	T=0.484
The Genome Aggregation Database	Other	Sub	302	G=0.390	T=0.610
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.504	T=0.495
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.429	T=0.571

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
rs1389733	0.00011	alcohol dependence	20201924

eQTL of rs1389733 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 rs1389733 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr9	14749409	14749496	E070	-42219
chr9	14749595	14751479	E070	-40236
chr9	14780671	14781233	E070	-10482
chr9	14781374	14781441	E070	-10274
chr9	14749595	14751479	E081	-40236
chr9	14774404	14774843	E081	-16872
chr9	14774983	14775058	E081	-16657
chr9	14775126	14775194	E081	-16521
chr9	14775873	14775987	E081	-15728
chr9	14776132	14776193	E081	-15522
chr9	14779230	14779335	E081	-12380
chr9	14780671	14781233	E081	-10482
chr9	14781374	14781441	E081	-10274
chr9	14781555	14781701	E081	-10014
chr9	14774404	14774843	E082	-16872
chr9	14774983	14775058	E082	-16657
chr9	14775126	14775194	E082	-16521
chr9	14780671	14781233	E082	-10482
chr9	14781374	14781441	E082	-10274
chr9	14781555	14781701	E082	-10014

rs1389733

Genomic Coordinates

Gene: FREM1, FRAS1 related extracellular matrix 1(minus strand)

Gene: LOC105375979, uncharacterized LOC105375979(plus strand): 2KB Upstream Variant

Population Frequency

P-Value

eQTL of rs1389733 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs1389733 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)