rs79246196

Homo sapiens
C>T
STAG3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0016 (482/29942,GnomAD)
T=0028 (828/29118,TOPMED)
T=0019 (93/5008,1000G)
T=0000 (0/3854,ALSPAC)
T=0001 (2/3708,TWINSUK)
chr7:100185286 (GRCh38.p7) (7q22.1)
AD
GWASCatalog
1   publication(s)
See rs on genome
119 Enhancers around
34 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.100185286C>T
GRCh37.p13 chr 7NC_000007.13:g.99782909C>T
STAG3 RefSeqGeneNG_034114.1:g.12563C>T

Gene: STAG3, stromal antigen 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
STAG3 transcript variant 2NM_001282716.1:c.N/AIntron Variant
STAG3 transcript variant 3NM_001282717.1:c.N/AIntron Variant
STAG3 transcript variant 4NM_001282718.1:c.N/AIntron Variant
STAG3 transcript variant 1NM_012447.3:c.N/AIntron Variant
STAG3 transcript variant X5XM_011515742.1:c.N/AIntron Variant
STAG3 transcript variant X1XM_017011683.1:c.N/AIntron Variant
STAG3 transcript variant X2XM_017011684.1:c.N/AIntron Variant
STAG3 transcript variant X3XM_017011685.1:c.N/AIntron Variant
STAG3 transcript variant X4XM_017011686.1:c.N/AIntron Variant
STAG3 transcript variant X6XM_017011687.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.932T=0.068
1000GenomesAmericanSub694C=1.000T=0.000
1000GenomesEast AsianSub1008C=1.000T=0.000
1000GenomesEuropeSub1006C=1.000T=0.000
1000GenomesGlobalStudy-wide5008C=0.981T=0.019
1000GenomesSouth AsianSub978C=1.000T=0.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=1.000T=0.000
The Genome Aggregation DatabaseAfricanSub8716C=0.945T=0.055
The Genome Aggregation DatabaseAmericanSub838C=1.000T=0.000
The Genome Aggregation DatabaseEast AsianSub1620C=1.000T=0.000
The Genome Aggregation DatabaseEuropeSub18466C=0.999T=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29942C=0.983T=0.016
The Genome Aggregation DatabaseOtherSub302C=1.000T=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.971T=0.028
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.999T=0.001
PMID Title Author Journal
29071344Genetic Risk Variants Associated With Comorbid Alcohol Dependence and Major Depression.Zhou HJAMA Psychiatry

P-Value

SNP ID p-value Traits Study
rs792461961E-06alcohol dependence29071344

eQTL of rs79246196 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 rs79246196 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 )
chr79974567099745733E067-37176
chr79975329599753453E067-29456
chr79975346299753705E067-29204
chr79975372699753851E067-29058
chr79975389699753963E067-28946
chr79975397899754658E067-28251
chr79976778599767993E067-14916
chr79976806999768167E067-14742
chr79976817999768275E067-14634
chr79976836399768563E067-14346
chr79977586099776015E067-6894
chr79979494899795023E06712039
chr79979509799795147E06712188
chr79979546099795514E06712551
chr79979568299795742E06712773
chr79977586099776015E068-6894
chr79979546099795514E06812551
chr79979568299795742E06812773
chr79980863799808723E06825728
chr79981340699813522E06830497
chr79981354199813923E06830632
chr79976806999768167E069-14742
chr79976817999768275E069-14634
chr79976836399768563E069-14346
chr79979568299795742E06912773
chr79979592199796468E06913012
chr79981291299813046E06930003
chr79981317599813253E06930266
chr79981340699813522E06930497
chr79981354199813923E06930632
chr79976683599767419E070-15490
chr79976750999767586E070-15323
chr79976761499767685E070-15224
chr79976778599767993E070-14916
chr79977162599771696E070-11213
chr79977171999771822E070-11087
chr79977190099771998E070-10911
chr79977202799772128E070-10781
chr79977213499772208E070-10701
chr79977220999772259E070-10650
chr79977229499772381E070-10528
chr79977257799772674E070-10235
chr79977275999772839E070-10070
chr79974798199748353E071-34556
chr79975008999750442E071-32467
chr79975097799751101E071-31808
chr79975128899751519E071-31390
chr79975152599751683E071-31226
chr79975169299752147E071-30762
chr79975216499752900E071-30009
chr79975397899754658E071-28251
chr79976683599767419E071-15490
chr79976750999767586E071-15323
chr79976761499767685E071-15224
chr79976778599767993E071-14916
chr79976806999768167E071-14742
chr79976817999768275E071-14634
chr79979546099795514E07112551
chr79979568299795742E07112773
chr79979592199796468E07113012
chr79981087699811073E07127967
chr79981113799811205E07128228
chr79981317599813253E07130266
chr79981340699813522E07130497
chr79981354199813923E07130632
chr79981393399814117E07131024
chr79981444199814588E07131532
chr79981468099814750E07131771
chr79976683599767419E072-15490
chr79976817999768275E072-14634
chr79976836399768563E072-14346
chr79979568299795742E07212773
chr79979592199796468E07213012
chr79975329599753453E073-29456
chr79975346299753705E073-29204
chr79975372699753851E073-29058
chr79975389699753963E073-28946
chr79975397899754658E073-28251
chr79976806999768167E073-14742
chr79976817999768275E073-14634
chr79976836399768563E073-14346
chr79979546099795514E07312551
chr79981206999812375E07329160
chr79981266299812784E07329753
chr79976683599767419E074-15490
chr79976806999768167E074-14742
chr79976817999768275E074-14634
chr79976836399768563E074-14346
chr79979546099795514E07412551
chr79979568299795742E07412773
chr79979592199796468E07413012
chr79981291299813046E07430003
chr79981317599813253E07430266
chr79981340699813522E07430497
chr79981354199813923E07430632
chr79981393399814117E07431024
chr79974798199748353E081-34556
chr79976683599767419E081-15490
chr79976750999767586E081-15323
chr79976761499767685E081-15224
chr79976778599767993E081-14916
chr79976806999768167E081-14742
chr79976817999768275E081-14634
chr79976836399768563E081-14346
chr79977257799772674E081-10235
chr79977275999772839E081-10070
chr79977353899773642E081-9267
chr79977369899773775E081-9134
chr79981280499812907E08129895
chr79981291299813046E08130003
chr79981317599813253E08130266
chr79981340699813522E08130497
chr79981354199813923E08130632
chr79974798199748353E082-34556
chr79977213499772208E082-10701
chr79977220999772259E082-10650
chr79977229499772381E082-10528
chr79977257799772674E082-10235
chr79977275999772839E082-10070










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr79974581599747448E067-35461
chr79975467899757151E067-25758
chr79977464999775834E067-7075
chr79974581599747448E068-35461
chr79975467899757151E068-25758
chr79977464999775834E068-7075
chr79974581599747448E069-35461
chr79975467899757151E069-25758
chr79976875199769348E069-13561
chr79977464999775834E069-7075
chr79974581599747448E070-35461
chr79975467899757151E070-25758
chr79976875199769348E070-13561
chr79977464999775834E070-7075
chr79974581599747448E071-35461
chr79975467899757151E071-25758
chr79976875199769348E071-13561
chr79977464999775834E071-7075
chr79974581599747448E072-35461
chr79975467899757151E072-25758
chr79976875199769348E072-13561
chr79977464999775834E072-7075
chr79974581599747448E073-35461
chr79975467899757151E073-25758
chr79977464999775834E073-7075
chr79974581599747448E074-35461
chr79975467899757151E074-25758
chr79976875199769348E074-13561
chr79977464999775834E074-7075
chr79974581599747448E081-35461
chr79974581599747448E082-35461
chr79975467899757151E082-25758
chr79976875199769348E082-13561
chr79977464999775834E082-7075