rs12348139

Homo sapiens
T>C
GLIS3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0078 (2347/29960,GnomAD)
C=0081 (2382/29118,TOPMED)
C=0065 (328/5008,1000G)
C=0070 (269/3854,ALSPAC)
C=0080 (298/3708,TWINSUK)
chr9:4232743 (GRCh38.p7) (9p24.2)
ND
GWASCatalog
1   publication(s)
See rs on genome
17 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.4232743T>C
GRCh37.p13 chr 9NC_000009.11:g.4232743T>C
GLIS3 RefSeqGeneNG_011782.1:g.72293A>G

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

Molecule type Change Amino acid[Codon] SO Term
GLIS3 transcript variant 1NM_001042413.1:c.N/AIntron Variant
GLIS3 transcript variant 2NM_152629.3:c.N/AGenic Upstream Transcript Variant
GLIS3 transcript variant X4XM_005251386.4:c.N/AIntron Variant
GLIS3 transcript variant X7XM_005251387.4:c.N/AIntron Variant
GLIS3 transcript variant X9XM_005251388.4:c.N/AIntron Variant
GLIS3 transcript variant X12XM_005251389.4:c.N/AIntron Variant
GLIS3 transcript variant X13XM_006716731.3:c.N/AIntron Variant
GLIS3 transcript variant X1XM_011517763.2:c.N/AIntron Variant
GLIS3 transcript variant X2XM_011517764.2:c.N/AIntron Variant
GLIS3 transcript variant X3XM_011517765.2:c.N/AIntron Variant
GLIS3 transcript variant X8XM_011517767.2:c.N/AIntron Variant
GLIS3 transcript variant X10XM_011517769.2:c.N/AIntron Variant
GLIS3 transcript variant X5XM_011517766.2:c.N/AGenic Upstream Transcript Variant
GLIS3 transcript variant X6XM_017014361.1:c.N/AGenic Upstream Transcript Variant
GLIS3 transcript variant X11XR_929206.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.911C=0.089
1000GenomesAmericanSub694T=0.940C=0.060
1000GenomesEast AsianSub1008T=0.933C=0.067
1000GenomesEuropeSub1006T=0.922C=0.078
1000GenomesGlobalStudy-wide5008T=0.935C=0.065
1000GenomesSouth AsianSub978T=0.980C=0.020
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.930C=0.070
The Genome Aggregation DatabaseAfricanSub8710T=0.900C=0.100
The Genome Aggregation DatabaseAmericanSub836T=0.960C=0.040
The Genome Aggregation DatabaseEast AsianSub1614T=0.929C=0.071
The Genome Aggregation DatabaseEuropeSub18498T=0.930C=0.069
The Genome Aggregation DatabaseGlobalStudy-wide29960T=0.921C=0.078
The Genome Aggregation DatabaseOtherSub302T=0.870C=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.918C=0.081
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.920C=0.080
PMID Title Author Journal
28440896Genome-wide meta-analysis identifies a novel susceptibility signal at CACNA2D3 for nicotine dependence.Yin XAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs123481391E-06nicotine dependence28440896

eQTL of rs12348139 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 rs12348139 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 )
chr942342514234301E0681508
chr942354434236733E0682700
chr942375894237670E0684846
chr942376834237723E0684940
chr942378424238924E0685099
chr942354434236733E0702700
chr942342514234301E0711508
chr942375894237670E0714846
chr942376834237723E0714940
chr942772684277404E07144525
chr942079354208546E073-24197
chr942745404274590E07341797
chr942071034207296E074-25447
chr942073164207425E074-25318
chr942075214207770E074-24973
chr942378424238924E0745099
chr942680294268079E08135286