rs10260238

Homo sapiens
C>T
ORC5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0088 (2658/29958,GnomAD)
T=0125 (3654/29118,TOPMED)
T=0100 (499/5008,1000G)
T=0056 (216/3854,ALSPAC)
T=0067 (248/3708,TWINSUK)
chr7:104196532 (GRCh38.p7) (7q22.1)
AD
GWASdb2
1   publication(s)
See rs on genome
34 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.104196532C>T
GRCh37.p13 chr 7NC_000007.13:g.103836980C>T
ORC5 RefSeqGeneNG_029899.1:g.16516G>A

Gene: ORC5, origin recognition complex, subunit 5(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ORC5 transcript variant 1NM_002553.3:c.N/AIntron Variant
ORC5 transcript variant 2NM_181747.3:c.N/AIntron Variant
ORC5 transcript variant X1XM_011516273.2:c.N/AIntron Variant
ORC5 transcript variant X2XR_001744792.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.765T=0.235
1000GenomesAmericanSub694C=0.940T=0.060
1000GenomesEast AsianSub1008C=0.999T=0.001
1000GenomesEuropeSub1006C=0.952T=0.048
1000GenomesGlobalStudy-wide5008C=0.900T=0.100
1000GenomesSouth AsianSub978C=0.900T=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.944T=0.056
The Genome Aggregation DatabaseAfricanSub8720C=0.786T=0.214
The Genome Aggregation DatabaseAmericanSub838C=0.970T=0.030
The Genome Aggregation DatabaseEast AsianSub1620C=0.999T=0.001
The Genome Aggregation DatabaseEuropeSub18478C=0.959T=0.040
The Genome Aggregation DatabaseGlobalStudy-wide29958C=0.911T=0.088
The Genome Aggregation DatabaseOtherSub302C=0.960T=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.874T=0.125
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.933T=0.067
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
rs102602380.000694alcohol dependence20201924

eQTL of rs10260238 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 rs10260238 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 )
chr7103871478103872454E06734498
chr7103815828103816012E069-20968
chr7103816168103816279E069-20701
chr7103816304103817170E069-19810
chr7103817466103817537E069-19443
chr7103871478103872454E06934498
chr7103870610103870675E07033630
chr7103880207103880262E07043227
chr7103880517103880571E07043537
chr7103880576103880616E07043596
chr7103880755103881436E07043775
chr7103883650103883731E07046670
chr7103883752103883812E07046772
chr7103884184103884247E07047204
chr7103816304103817170E071-19810
chr7103817466103817537E072-19443
chr7103871478103872454E07234498
chr7103883650103883731E07346670
chr7103871478103872454E07434498
chr7103871104103871367E08134124
chr7103871478103872454E08134498
chr7103880207103880262E08143227
chr7103880517103880571E08143537
chr7103880576103880616E08143596
chr7103880755103881436E08143775
chr7103883650103883731E08146670
chr7103883752103883812E08146772
chr7103884184103884247E08147204
chr7103871104103871367E08234124
chr7103880576103880616E08243596
chr7103880755103881436E08243775
chr7103883650103883731E08246670
chr7103883752103883812E08246772
chr7103884184103884247E08247204









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr7103847408103849279E06710428
chr7103847408103849279E06810428
chr7103847408103849279E06910428
chr7103847408103849279E07010428
chr7103847408103849279E07110428
chr7103847408103849279E07210428
chr7103847408103849279E07310428
chr7103847408103849279E07410428
chr7103847408103849279E08110428
chr7103847408103849279E08210428