rs6459707

Homo sapiens
C>T
CNPY1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0407 (12181/29886,GnomAD)
C==0384 (11198/29118,TOPMED)
C==0402 (2012/5008,1000G)
C==0436 (1682/3854,ALSPAC)
C==0435 (1612/3708,TWINSUK)
chr7:155512409 (GRCh38.p7) (7q36.3)
ND
GWASdb2
1   publication(s)
See rs on genome
17 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.155512409C>T
GRCh37.p13 chr 7NC_000007.13:g.155305104C>T

Gene: CNPY1, canopy FGF signaling regulator 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CNPY1 transcriptNM_001103176.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.315T=0.685
1000GenomesAmericanSub694C=0.310T=0.690
1000GenomesEast AsianSub1008C=0.463T=0.537
1000GenomesEuropeSub1006C=0.445T=0.555
1000GenomesGlobalStudy-wide5008C=0.402T=0.598
1000GenomesSouth AsianSub978C=0.480T=0.520
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.436T=0.564
The Genome Aggregation DatabaseAfricanSub8698C=0.340T=0.660
The Genome Aggregation DatabaseAmericanSub836C=0.280T=0.720
The Genome Aggregation DatabaseEast AsianSub1610C=0.509T=0.491
The Genome Aggregation DatabaseEuropeSub18440C=0.436T=0.564
The Genome Aggregation DatabaseGlobalStudy-wide29886C=0.407T=0.592
The Genome Aggregation DatabaseOtherSub302C=0.430T=0.570
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.384T=0.615
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.435T=0.565
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs64597078.49E-06alcohol and nictotine co-dependence20158304

eQTL of rs6459707 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 rs6459707 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 )
chr7155276397155276515E067-28589
chr7155276565155277081E067-28023
chr7155263120155263170E070-41934
chr7155275978155276024E070-29080
chr7155276062155276326E070-28778
chr7155276397155276515E070-28589
chr7155335054155335108E07029950
chr7155335163155335215E07030059
chr7155335326155335376E07030222
chr7155335913155336477E07030809
chr7155336578155336660E07031474
chr7155276565155277081E071-28023
chr7155314800155314850E0819696
chr7155315467155315961E08110363
chr7155316041155316082E08110937
chr7155347910155348351E08142806
chr7155348392155348442E08143288




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr7155325547155326842E06720443
chr7155283071155284614E068-20490
chr7155325547155326842E06920443
chr7155283071155284614E071-20490
chr7155283071155284614E072-20490
chr7155283071155284614E073-20490
chr7155283071155284614E074-20490
chr7155325547155326842E07420443
chr7155302445155303458E082-1646