rs9636470

Homo sapiens
T>C / T>G
RGPD2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0000 (1/29116,TOPMED)
C=0127 (2625/20674,GnomAD)
chr2:87866942 (GRCh38.p7) (2p11.2)
ND
GWASCatalog
2   publication(s)
See rs on genome
72 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.87866942T>C
GRCh38.p7 chr 2NC_000002.12:g.87866942T>G
GRCh37.p13 chr 2NC_000002.11:g.88166461T>C
GRCh37.p13 chr 2NC_000002.11:g.88166461T>G

Gene: RGPD2, RANBP2-like and GRIP domain containing 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
RGPD2 transcriptNM_001078170.2:c.N/AGenic Upstream Transcript Variant
RGPD2 transcript variant X1XM_017004845.1:c.N/AIntron Variant
RGPD2 transcript variant X5XM_017004848.1:c.N/AIntron Variant
RGPD2 transcript variant X6XM_017004849.1:c.N/AIntron Variant
RGPD2 transcript variant X7XM_017004850.1:c.N/AIntron Variant
RGPD2 transcript variant X2XM_017004846.1:c.N/AGenic Upstream Transcript Variant
RGPD2 transcript variant X3XM_017004847.1:c.N/AGenic Upstream Transcript Variant
RGPD2 transcript variant X4XR_001738923.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
The Genome Aggregation DatabaseAfricanSub7010T=0.961C=0.039
The Genome Aggregation DatabaseAmericanSub568T=0.860C=0.140
The Genome Aggregation DatabaseEast AsianSub1022T=0.787C=0.213
The Genome Aggregation DatabaseEuropeSub11874T=0.830C=0.170
The Genome Aggregation DatabaseGlobalStudy-wide20674T=0.873C=0.127
The Genome Aggregation DatabaseOtherSub200T=0.810C=0.200
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=1.000G=0.000
PMID Title Author Journal
22362730Unrecognized sequence homologies may confound genome-wide association studies.Galichon PNucleic Acids Res
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs96364703E-08alcohol and nicotine co-dependence22488850

eQTL of rs9636470 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 rs9636470 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 )
chr24256875042568979E067-20623
chr24256923742569386E067-20216
chr24256942442570292E067-19310
chr24257329042573354E067-16248
chr24257340242573499E067-16103
chr24256581542565965E068-23637
chr24256609042566249E068-23353
chr24256642342566626E068-22976
chr24256682542566985E068-22617
chr24256761442567698E068-21904
chr24256774442567784E068-21818
chr24256786842567940E068-21662
chr24256807742568185E068-21417
chr24256875042568979E068-20623
chr24256923742569386E068-20216
chr24256942442570292E068-19310
chr24257295542573005E068-16597
chr24257329042573354E068-16248
chr24257340242573499E068-16103
chr24258108542581168E068-8434
chr24258957242589669E0680
chr24259480342594879E0685201
chr24259490642595040E0685304
chr24259909342599742E0689491
chr24256581542565965E069-23637
chr24256875042568979E069-20623
chr24256923742569386E069-20216
chr24256942442570292E069-19310
chr24257295542573005E069-16597
chr24257340242573499E069-16103
chr24256642342566626E071-22976
chr24256682542566985E071-22617
chr24256761442567698E071-21904
chr24256774442567784E071-21818
chr24256786842567940E071-21662
chr24256807742568185E071-21417
chr24256875042568979E071-20623
chr24256923742569386E071-20216
chr24256942442570292E071-19310
chr24257295542573005E071-16597
chr24257329042573354E071-16248
chr24257340242573499E071-16103
chr24256609042566249E072-23353
chr24256642342566626E072-22976
chr24256682542566985E072-22617
chr24256761442567698E072-21904
chr24256774442567784E072-21818
chr24256786842567940E072-21662
chr24256807742568185E072-21417
chr24256875042568979E072-20623
chr24256923742569386E072-20216
chr24256942442570292E072-19310
chr24257295542573005E072-16597
chr24257329042573354E072-16248
chr24257340242573499E072-16103
chr24258108542581168E072-8434
chr24256875042568979E073-20623
chr24256923742569386E073-20216
chr24256942442570292E073-19310
chr24259653742596633E0736935
chr24259670042596929E0737098
chr24256552442565610E074-23992
chr24256581542565965E074-23637
chr24256609042566249E074-23353
chr24256807742568185E074-21417
chr24256875042568979E074-20623
chr24256923742569386E074-20216
chr24256942442570292E074-19310
chr24257295542573005E074-16597
chr24257329042573354E074-16248
chr24257340242573499E074-16103
chr24258108542581168E074-8434







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr24258686842587613E067-1989
chr24258769142589488E067-114
chr24258686842587613E068-1989
chr24258769142589488E068-114
chr24258686842587613E069-1989
chr24258769142589488E069-114
chr24258686842587613E070-1989
chr24258769142589488E070-114
chr24258686842587613E071-1989
chr24258769142589488E071-114
chr24258686842587613E072-1989
chr24258769142589488E072-114
chr24258686842587613E073-1989
chr24258769142589488E073-114
chr24258686842587613E074-1989
chr24258769142589488E074-114
chr24258686842587613E081-1989
chr24258769142589488E081-114
chr24258686842587613E082-1989
chr24258769142589488E082-114