rs7851070

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

GLIS3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0387 (11589/29886,GnomAD)
G=0317 (9256/29118,TOPMED)
G=0393 (1969/5008,1000G)
G=0455 (1753/3854,ALSPAC)
G=0453 (1678/3708,TWINSUK)

Position: chr9:4170457 (GRCh38.p7) (9p24.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 63 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.4170457A>G
GRCh37.p13 chr 9	NC_000009.11:g.4170457A>G
GLIS3 RefSeqGene	NG_011782.1:g.134579T>C

Gene: GLIS3, GLIS family zinc finger 3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GLIS3 transcript variant 1	NM_001042413.1:c.	N/A	Intron Variant
GLIS3 transcript variant 2	NM_152629.3:c.	N/A	Genic Upstream Transcript Variant
GLIS3 transcript variant X4	XM_005251386.4:c.	N/A	Intron Variant
GLIS3 transcript variant X7	XM_005251387.4:c.	N/A	Intron Variant
GLIS3 transcript variant X9	XM_005251388.4:c.	N/A	Intron Variant
GLIS3 transcript variant X12	XM_005251389.4:c.	N/A	Intron Variant
GLIS3 transcript variant X13	XM_006716731.3:c.	N/A	Intron Variant
GLIS3 transcript variant X1	XM_011517763.2:c.	N/A	Intron Variant
GLIS3 transcript variant X2	XM_011517764.2:c.	N/A	Intron Variant
GLIS3 transcript variant X3	XM_011517765.2:c.	N/A	Intron Variant
GLIS3 transcript variant X8	XM_011517767.2:c.	N/A	Intron Variant
GLIS3 transcript variant X10	XM_011517769.2:c.	N/A	Intron Variant
GLIS3 transcript variant X5	XM_011517766.2:c.	N/A	Genic Upstream Transcript Variant
GLIS3 transcript variant X6	XM_017014361.1:c.	N/A	Genic Upstream Transcript Variant
GLIS3 transcript variant X11	XR_929206.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.911	G=0.089
1000Genomes	American	Sub	694	A=0.490	G=0.510
1000Genomes	East Asian	Sub	1008	A=0.359	G=0.641
1000Genomes	Europe	Sub	1006	A=0.557	G=0.443
1000Genomes	Global	Study-wide	5008	A=0.607	G=0.393
1000Genomes	South Asian	Sub	978	A=0.580	G=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.545	G=0.455
The Genome Aggregation Database	African	Sub	8714	A=0.859	G=0.141
The Genome Aggregation Database	American	Sub	834	A=0.470	G=0.530
The Genome Aggregation Database	East Asian	Sub	1610	A=0.333	G=0.667
The Genome Aggregation Database	Europe	Sub	18426	A=0.527	G=0.472
The Genome Aggregation Database	Global	Study-wide	29886	A=0.612	G=0.387
The Genome Aggregation Database	Other	Sub	302	A=0.570	G=0.430
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.682	G=0.317
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.547	G=0.453

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs7851070	7.02E-06	alcohol and nictotine co-dependence	20158304

eQTL of rs7851070 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 rs7851070 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 )
chr9	4145455	4145538	E068	-24919
chr9	4147369	4148411	E068	-22046
chr9	4148824	4148959	E068	-21498
chr9	4174577	4174804	E068	4120
chr9	4174853	4175113	E068	4396
chr9	4175178	4175258	E068	4721
chr9	4175340	4175485	E068	4883
chr9	4175562	4175668	E068	5105
chr9	4175702	4175804	E068	5245
chr9	4130440	4130490	E069	-39967
chr9	4131921	4131971	E069	-38486
chr9	4132085	4132488	E069	-37969
chr9	4147369	4148411	E069	-22046
chr9	4164860	4164992	E069	-5465
chr9	4165605	4165663	E069	-4794
chr9	4157665	4158296	E070	-12161
chr9	4147369	4148411	E071	-22046
chr9	4132578	4132664	E072	-37793
chr9	4145455	4145538	E073	-24919
chr9	4150477	4150548	E073	-19909
chr9	4175340	4175485	E073	4883
chr9	4175562	4175668	E073	5105
chr9	4175702	4175804	E073	5245
chr9	4175946	4176108	E073	5489
chr9	4178152	4178712	E073	7695
chr9	4207935	4208546	E073	37478
chr9	4147070	4147143	E074	-23314
chr9	4147369	4148411	E074	-22046
chr9	4165839	4165894	E074	-4563
chr9	4166346	4166436	E074	-4021
chr9	4207103	4207296	E074	36646
chr9	4207316	4207425	E074	36859
chr9	4207521	4207770	E074	37064
chr9	4143041	4143095	E081	-27362
chr9	4147369	4148411	E081	-22046
chr9	4156363	4156458	E081	-13999
chr9	4157371	4157476	E081	-12981
chr9	4157665	4158296	E081	-12161
chr9	4158901	4159011	E081	-11446
chr9	4159087	4159139	E081	-11318
chr9	4167784	4167863	E081	-2594
chr9	4167891	4168024	E081	-2433
chr9	4168031	4168269	E081	-2188
chr9	4168340	4168845	E081	-1612
chr9	4169185	4169293	E081	-1164
chr9	4170988	4171038	E081	531
chr9	4171096	4171205	E081	639
chr9	4171264	4171871	E081	807
chr9	4172575	4172619	E081	2118
chr9	4172628	4172718	E081	2171
chr9	4172802	4173163	E081	2345
chr9	4173392	4173468	E081	2935
chr9	4174058	4174131	E081	3601
chr9	4174466	4174516	E081	4009
chr9	4174577	4174804	E081	4120
chr9	4174853	4175113	E081	4396
chr9	4175178	4175258	E081	4721
chr9	4175340	4175485	E081	4883
chr9	4175562	4175668	E081	5105
chr9	4175702	4175804	E081	5245
chr9	4175946	4176108	E081	5489
chr9	4158901	4159011	E082	-11446
chr9	4159087	4159139	E082	-11318