rs6089556

Homo sapiens
T>C
CDH4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0496 (14869/29924,GnomAD)
C=0455 (13255/29118,TOPMED)
T==0419 (2099/5008,1000G)
T==0480 (1849/3854,ALSPAC)
T==0485 (1800/3708,TWINSUK)
chr20:61929031 (GRCh38.p7) (20q13.33)
ND
GWASdb2
1   publication(s)
See rs on genome
88 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.61929031T>C
GRCh37.p13 chr 20NC_000020.10:g.60504089T>C
GRCh38.p7 chr 20 alt locus HSCHR20_1_CTG2NT_187623.1:g.42709C>T

Gene: CDH4, cadherin 4(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CDH4 transcript variant 2NM_001252338.2:c.N/AIntron Variant
CDH4 transcript variant 3NM_001252339.2:c.N/AIntron Variant
CDH4 transcript variant 1NM_001794.4:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.701C=0.299
1000GenomesAmericanSub694T=0.420C=0.580
1000GenomesEast AsianSub1008T=0.159C=0.841
1000GenomesEuropeSub1006T=0.474C=0.526
1000GenomesGlobalStudy-wide5008T=0.419C=0.581
1000GenomesSouth AsianSub978T=0.250C=0.750
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.480C=0.520
The Genome Aggregation DatabaseAfricanSub8710T=0.649C=0.351
The Genome Aggregation DatabaseAmericanSub838T=0.370C=0.630
The Genome Aggregation DatabaseEast AsianSub1618T=0.148C=0.852
The Genome Aggregation DatabaseEuropeSub18458T=0.460C=0.539
The Genome Aggregation DatabaseGlobalStudy-wide29924T=0.496C=0.503
The Genome Aggregation DatabaseOtherSub300T=0.550C=0.450
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.544C=0.455
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.485C=0.515
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs60895560.000473nicotine smoking19268276

eQTL of rs6089556 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 rs6089556 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 )
chr206047110660472084E068-32005
chr206046221360462584E069-41505
chr206046263360462901E069-41188
chr206047110660472084E069-32005
chr206052935560529408E06925266
chr206055075760550811E06946668
chr206055088860550999E06946799
chr206055100460551082E06946915
chr206055112360551482E06947034
chr206055160360551653E06947514
chr206055177960551864E06947690
chr206046965460469704E070-34385
chr206047518060475277E070-28812
chr206047533860475647E070-28442
chr206047577560475942E070-28147
chr206051447660514526E07010387
chr206052443960524519E07020350
chr206052462560524669E07020536
chr206052469460524819E07020605
chr206052487060524924E07020781
chr206052546860525554E07021379
chr206052570060525835E07021611
chr206052608360526202E07021994
chr206052659260527000E07022503
chr206052701260527345E07022923
chr206052935560529408E07025266
chr206054963460549684E07045545
chr206055039760550509E07046308
chr206055112360551482E07047034
chr206055160360551653E07047514
chr206055177960551864E07047690
chr206055204760552127E07047958
chr206055223160552405E07048142
chr206055246260552621E07048373
chr206055272360552795E07048634
chr206047110660472084E071-32005
chr206055160360551653E07147514
chr206055177960551864E07147690
chr206055204760552127E07147958
chr206055223160552405E07148142
chr206055246260552621E07148373
chr206047110660472084E072-32005
chr206053980360539911E07235714
chr206054516260545221E07241073
chr206054764860547698E07243559
chr206054775060548001E07243661
chr206054813860548213E07244049
chr206055160360551653E07247514
chr206055177960551864E07247690
chr206055204760552127E07247958
chr206055223160552405E07248142
chr206055246260552621E07248373
chr206053980360539911E07335714
chr206054516260545221E07341073
chr206055100460551082E07346915
chr206055112360551482E07347034
chr206055160360551653E07347514
chr206055177960551864E07347690
chr206047110660472084E074-32005
chr206054516260545221E07441073
chr206055112360551482E07447034
chr206055160360551653E07447514
chr206055177960551864E07447690
chr206046221360462584E081-41505
chr206046263360462901E081-41188
chr206051565060515928E08111561
chr206051599560516075E08111906
chr206051615660516236E08112067
chr206051626060516383E08112171
chr206052546860525554E08121379
chr206052570060525835E08121611
chr206052659260527000E08122503
chr206052701260527345E08122923
chr206052748760527636E08123398
chr206053373660534017E08129647
chr206053408960534799E08130000
chr206054813860548213E08144049
chr206055160360551653E08147514
chr206055177960551864E08147690
chr206055204760552127E08147958
chr206055223160552405E08148142
chr206055246260552621E08148373
chr206055272360552795E08148634
chr206055290860552975E08148819
chr206046210660462195E082-41894
chr206053347160533664E08229382
chr206053373660534017E08229647
chr206055272360552795E08248634