rs9828473

Homo sapiens
G>A
SETD2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0038 (1144/29966,GnomAD)
A=0057 (1669/29118,TOPMED)
A=0041 (206/5008,1000G)
A=0001 (3/3854,ALSPAC)
A=0001 (3/3708,TWINSUK)
chr3:47118198 (GRCh38.p7) (3p21.31)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.47118198G>A
GRCh37.p13 chr 3NC_000003.11:g.47159688G>A
SETD2 RefSeqGene LRG_775

Gene: SETD2, SET domain containing 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SETD2 transcript variant 1NM_014159.6:c.N/AIntron Variant
SETD2 transcript variant X1XM_011533631.2:c.N/AIntron Variant
SETD2 transcript variant X2XM_011533632.2:c.N/AIntron Variant
SETD2 transcript variant X3XM_011533633.2:c.N/AIntron Variant
SETD2 transcript variant X2XM_011533634.1:c.N/AIntron Variant
SETD2 transcript variant X5XM_017006270.1:c.N/AIntron Variant
SETD2 transcript variant X7XR_001740125.1:n.N/AIntron Variant
SETD2 transcript variant X8XR_001740126.1:n.N/AIntron Variant
SETD2 transcript variant X9XR_001740127.1:n.N/AIntron Variant
SETD2 transcript variant X10XR_001740128.1:n.N/AIntron Variant
SETD2 transcript variant X11XR_001740129.1:n.N/AIntron Variant
SETD2 transcript variant X12XR_001740130.1:n.N/AIntron Variant
SETD2 transcript variant X13XR_001740131.1:n.N/AIntron Variant
SETD2 transcript variant X14XR_001740132.1:n.N/AIntron Variant
SETD2 transcript variant X15XR_001740133.1:n.N/AIntron Variant
SETD2 transcript variant X6XR_940418.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.856A=0.144
1000GenomesAmericanSub694G=0.980A=0.020
1000GenomesEast AsianSub1008G=1.000A=0.000
1000GenomesEuropeSub1006G=0.998A=0.002
1000GenomesGlobalStudy-wide5008G=0.959A=0.041
1000GenomesSouth AsianSub978G=1.000A=0.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.999A=0.001
The Genome Aggregation DatabaseAfricanSub8720G=0.871A=0.129
The Genome Aggregation DatabaseAmericanSub836G=0.990A=0.010
The Genome Aggregation DatabaseEast AsianSub1622G=1.000A=0.000
The Genome Aggregation DatabaseEuropeSub18486G=0.999A=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29966G=0.961A=0.038
The Genome Aggregation DatabaseOtherSub302G=0.990A=0.010
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.942A=0.057
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.999A=0.001
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs98284730.000684alcohol dependence20201924

eQTL of rs9828473 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 rs9828473 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 )
chr34711489447115056E067-44632
chr34718277447182917E06723086
chr34718295647183059E06723268
chr34718321647183292E06723528
chr34718355847183619E06723870
chr34718362647183683E06723938
chr34719104447191084E06731356
chr34719419347194397E06734505
chr34719440147194552E06734713
chr34720097447201199E06741286
chr34720152347201589E06741835
chr34720243347202483E06742745
chr34720259447202658E06742906
chr34720293847203004E06743250
chr34716973647169944E06810048
chr34717007847170128E06810390
chr34717748447177544E06817796
chr34717757647177656E06817888
chr34718250247182609E06822814
chr34718277447182917E06823086
chr34718295647183059E06823268
chr34718321647183292E06823528
chr34718355847183619E06823870
chr34718362647183683E06823938
chr34719104447191084E06831356
chr34719409847194138E06834410
chr34719419347194397E06834505
chr34719440147194552E06834713
chr34719781347198038E06838125
chr34719991347199987E06840225
chr34720097447201199E06841286
chr34720152347201589E06841835
chr34720243347202483E06842745
chr34720259447202658E06842906
chr34720293847203004E06843250
chr34720783647207876E06848148
chr34720789047207944E06848202
chr34720798247208112E06848294
chr34711818247118357E069-41331
chr34718295647183059E06923268
chr34718321647183292E06923528
chr34718355847183619E06923870
chr34720097447201199E06941286
chr34720152347201589E06941835
chr34720243347202483E06942745
chr34720259447202658E06942906
chr34720293847203004E06943250
chr34720760047207717E06947912
chr34720783647207876E06948148
chr34720789047207944E06948202
chr34720798247208112E06948294
chr34720097447201199E07041286
chr34720152347201589E07041835
chr34720243347202483E07042745
chr34720259447202658E07042906
chr34720293847203004E07043250
chr34720760047207717E07047912
chr34720783647207876E07048148
chr34720789047207944E07048202
chr34720798247208112E07048294
chr34711818247118357E071-41331
chr34717748447177544E07117796
chr34717757647177656E07117888
chr34719419347194397E07134505
chr34719440147194552E07134713
chr34719809047198140E07138402
chr34720097447201199E07141286
chr34720152347201589E07141835
chr34720243347202483E07142745
chr34720259447202658E07142906
chr34720293847203004E07143250
chr34720760047207717E07147912
chr34720783647207876E07148148
chr34720789047207944E07148202
chr34720798247208112E07148294
chr34716973647169944E07210048
chr34718355847183619E07223870
chr34718362647183683E07223938
chr34720097447201199E07241286
chr34720152347201589E07241835
chr34720243347202483E07242745
chr34720259447202658E07242906
chr34720293847203004E07243250
chr34718355847183619E07323870
chr34718362647183683E07323938
chr34719781347198038E07338125
chr34719809047198140E07338402
chr34720097447201199E07341286
chr34720152347201589E07341835
chr34720243347202483E07342745
chr34720259447202658E07342906
chr34720293847203004E07343250
chr34711818247118357E074-41331
chr34717757647177656E07417888
chr34717782747177890E07418139
chr34718355847183619E07423870
chr34718362647183683E07423938
chr34719809047198140E07438402
chr34719991347199987E07440225
chr34720097447201199E07441286
chr34720152347201589E07441835
chr34720243347202483E07442745
chr34720259447202658E07442906
chr34720293847203004E07443250
chr34720760047207717E07447912
chr34720783647207876E07448148
chr34720789047207944E07448202
chr34720798247208112E07448294
chr34720097447201199E08141286
chr34720152347201589E08141835
chr34720243347202483E08142745
chr34720259447202658E08142906
chr34720293847203004E08143250
chr34720097447201199E08241286
chr34720152347201589E08241835
chr34720243347202483E08242745
chr34720259447202658E08242906
chr34720293847203004E08243250
chr34720783647207876E08248148
chr34720789047207944E08248202
chr34720798247208112E08248294










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr34720407547206877E06744387
chr34720712647207185E06747438
chr34720407547206877E06844387
chr34720407547206877E06944387
chr34720407547206877E07044387
chr34720712647207185E07047438
chr34720407547206877E07144387
chr34720712647207185E07147438
chr34720407547206877E07244387
chr34720407547206877E07344387
chr34720712647207185E07347438
chr34720407547206877E07444387
chr34720407547206877E08144387
chr34720407547206877E08244387
chr34720712647207185E08247438