rs7858348

Homo sapiens
G>A
USP20 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0123 (3689/29922,GnomAD)
G==0173 (5059/29118,TOPMED)
G==0127 (634/5008,1000G)
G==0117 (451/3854,ALSPAC)
G==0117 (435/3708,TWINSUK)
chr9:129855609 (GRCh38.p7) (9q34.11)
AD
GWASdb2
1   publication(s)
See rs on genome
109 Enhancers around
38 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.129855609G>A
GRCh37.p13 chr 9NC_000009.11:g.132617888G>A
USP20 RefSeqGeneNG_033097.1:g.25193G>A

Gene: USP20, ubiquitin specific peptidase 20(plus strand)

Molecule type Change Amino acid[Codon] SO Term
USP20 transcript variant 2NM_001008563.4:c.N/AIntron Variant
USP20 transcript variant 3NM_001110303.3:c.N/AIntron Variant
USP20 transcript variant 1NM_006676.7:c.N/AIntron Variant
USP20 transcript variant X3XM_005251665.3:c.N/AIntron Variant
USP20 transcript variant X1XM_011518161.2:c.N/AIntron Variant
USP20 transcript variant X2XM_011518162.2:c.N/AIntron Variant
USP20 transcript variant X4XM_005251666.3:c.N/AGenic Upstream Transcript Variant
USP20 transcript variant X5XM_017014221.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.266A=0.734
1000GenomesAmericanSub694G=0.100A=0.900
1000GenomesEast AsianSub1008G=0.017A=0.983
1000GenomesEuropeSub1006G=0.091A=0.909
1000GenomesGlobalStudy-wide5008G=0.127A=0.873
1000GenomesSouth AsianSub978G=0.110A=0.890
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.117A=0.883
The Genome Aggregation DatabaseAfricanSub8700G=0.230A=0.770
The Genome Aggregation DatabaseAmericanSub838G=0.060A=0.940
The Genome Aggregation DatabaseEast AsianSub1618G=0.021A=0.979
The Genome Aggregation DatabaseEuropeSub18464G=0.084A=0.915
The Genome Aggregation DatabaseGlobalStudy-wide29922G=0.123A=0.876
The Genome Aggregation DatabaseOtherSub302G=0.150A=0.850
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.173A=0.826
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.117A=0.883
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs78583480.000983alcohol dependence21314694

eQTL of rs7858348 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 rs7858348 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 )
chr9132571412132571477E067-46411
chr9132571743132571826E067-46062
chr9132571989132572039E067-45849
chr9132584934132585079E067-32809
chr9132599376132599452E067-18436
chr9132599521132599752E067-18136
chr9132599839132599915E067-17973
chr9132600192132600326E067-17562
chr9132664285132664367E06746397
chr9132664400132664447E06746512
chr9132664768132664861E06746880
chr9132599199132599271E068-18617
chr9132599376132599452E068-18436
chr9132599521132599752E068-18136
chr9132600905132601394E068-16494
chr9132601411132601456E068-16432
chr9132601459132601655E068-16233
chr9132601732132601796E068-16092
chr9132602014132602127E068-15761
chr9132628432132629793E06810544
chr9132656232132657077E06838344
chr9132664285132664367E06846397
chr9132664400132664447E06846512
chr9132664768132664861E06846880
chr9132567910132567964E069-49924
chr9132567969132568037E069-49851
chr9132599376132599452E069-18436
chr9132599521132599752E069-18136
chr9132599839132599915E069-17973
chr9132600192132600326E069-17562
chr9132645953132646134E06928065
chr9132655082132655150E06937194
chr9132655241132655550E06937353
chr9132656232132657077E06938344
chr9132664285132664367E06946397
chr9132664400132664447E06946512
chr9132664768132664861E06946880
chr9132664938132664986E06947050
chr9132665030132665148E06947142
chr9132596007132596061E070-21827
chr9132596123132596177E070-21711
chr9132599199132599271E070-18617
chr9132599376132599452E070-18436
chr9132600905132601394E070-16494
chr9132601411132601456E070-16432
chr9132601459132601655E070-16233
chr9132601732132601796E070-16092
chr9132602014132602127E070-15761
chr9132567910132567964E071-49924
chr9132596007132596061E071-21827
chr9132596123132596177E071-21711
chr9132599199132599271E071-18617
chr9132599376132599452E071-18436
chr9132655082132655150E07137194
chr9132655241132655550E07137353
chr9132655662132655722E07137774
chr9132655795132655883E07137907
chr9132656232132657077E07138344
chr9132664285132664367E07146397
chr9132664400132664447E07146512
chr9132664768132664861E07146880
chr9132664938132664986E07147050
chr9132665030132665148E07147142
chr9132665217132665291E07147329
chr9132599376132599452E072-18436
chr9132599521132599752E072-18136
chr9132603483132603587E072-14301
chr9132603709132603798E072-14090
chr9132603810132603903E072-13985
chr9132655082132655150E07237194
chr9132655241132655550E07237353
chr9132656232132657077E07238344
chr9132664285132664367E07246397
chr9132664400132664447E07246512
chr9132664768132664861E07246880
chr9132664938132664986E07247050
chr9132665030132665148E07247142
chr9132584934132585079E073-32809
chr9132600905132601394E073-16494
chr9132601411132601456E073-16432
chr9132601459132601655E073-16233
chr9132601732132601796E073-16092
chr9132602014132602127E073-15761
chr9132627631132627706E0739743
chr9132664285132664367E07346397
chr9132664400132664447E07346512
chr9132664768132664861E07346880
chr9132599199132599271E074-18617
chr9132645953132646134E07428065
chr9132655082132655150E07437194
chr9132655241132655550E07437353
chr9132664120132664169E07446232
chr9132664285132664367E07446397
chr9132664400132664447E07446512
chr9132664768132664861E07446880
chr9132664938132664986E07447050
chr9132665030132665148E07447142
chr9132665217132665291E07447329
chr9132599199132599271E081-18617
chr9132655082132655150E08137194
chr9132655241132655550E08137353
chr9132655662132655722E08137774
chr9132655795132655883E08137907
chr9132656232132657077E08138344
chr9132569391132569673E082-48215
chr9132569707132569758E082-48130
chr9132599199132599271E082-18617
chr9132599376132599452E082-18436
chr9132599521132599752E082-18136










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr9132585841132585941E067-31947
chr9132585991132586650E067-31238
chr9132586697132586801E067-31087
chr9132596768132599190E067-18698
chr9132585841132585941E068-31947
chr9132585991132586650E068-31238
chr9132586697132586801E068-31087
chr9132596768132599190E068-18698
chr9132585841132585941E069-31947
chr9132585991132586650E069-31238
chr9132586697132586801E069-31087
chr9132596768132599190E069-18698
chr9132585841132585941E070-31947
chr9132585991132586650E070-31238
chr9132586697132586801E070-31087
chr9132596768132599190E070-18698
chr9132585841132585941E071-31947
chr9132585991132586650E071-31238
chr9132586697132586801E071-31087
chr9132596768132599190E071-18698
chr9132585841132585941E072-31947
chr9132585991132586650E072-31238
chr9132586697132586801E072-31087
chr9132596768132599190E072-18698
chr9132585841132585941E073-31947
chr9132585991132586650E073-31238
chr9132586697132586801E073-31087
chr9132596768132599190E073-18698
chr9132585841132585941E074-31947
chr9132585991132586650E074-31238
chr9132586697132586801E074-31087
chr9132596768132599190E074-18698
chr9132596768132599190E081-18698
chr9132585841132585941E082-31947
chr9132585991132586650E082-31238
chr9132586697132586801E082-31087
chr9132586833132586934E082-30954
chr9132596768132599190E082-18698