rs11707897

Homo sapiens
T>C
CNTN4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0137 (4105/29964,GnomAD)
C=0111 (3244/29118,TOPMED)
C=0090 (451/5008,1000G)
C=0162 (625/3854,ALSPAC)
C=0183 (678/3708,TWINSUK)
chr3:2572942 (GRCh38.p7) (3p26.3)
ND | AD
GWASdb2
3   publication(s)
See rs on genome
15 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.2572942T>C
GRCh37.p13 chr 3NC_000003.11:g.2614626T>C
CNTN4 RefSeqGeneNG_012827.1:g.477380T>C

Gene: CNTN4, contactin 4(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CNTN4 transcript variant 4NM_001206955.1:c.N/AIntron Variant
CNTN4 transcript variant 1NM_175607.2:c.N/AIntron Variant
CNTN4 transcript variant 5NM_001206956.1:c.N/AGenic Upstream Transcript Variant
CNTN4 transcript variant 3NM_175613.2:c.N/AGenic Upstream Transcript Variant
CNTN4 transcript variant X11XM_006713004.3:c.N/AIntron Variant
CNTN4 transcript variant X2XM_011533425.2:c.N/AIntron Variant
CNTN4 transcript variant X4XM_011533426.2:c.N/AIntron Variant
CNTN4 transcript variant X4XM_011533427.2:c.N/AIntron Variant
CNTN4 transcript variant X6XM_011533428.2:c.N/AIntron Variant
CNTN4 transcript variant X8XM_011533429.2:c.N/AIntron Variant
CNTN4 transcript variant X7XM_011533430.2:c.N/AIntron Variant
CNTN4 transcript variant X1XM_017005782.1:c.N/AIntron Variant
CNTN4 transcript variant X3XM_017005783.1:c.N/AIntron Variant
CNTN4 transcript variant X6XM_017005784.1:c.N/AIntron Variant
CNTN4 transcript variant X9XM_017005785.1:c.N/AIntron Variant
CNTN4 transcript variant X11XM_017005786.1:c.N/AIntron Variant
CNTN4 transcript variant X12XM_017005787.1:c.N/AIntron Variant
CNTN4 transcript variant X15XM_017005788.1:c.N/AIntron Variant
CNTN4 transcript variant X13XM_011533431.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.967C=0.033
1000GenomesAmericanSub694T=0.920C=0.080
1000GenomesEast AsianSub1008T=0.974C=0.026
1000GenomesEuropeSub1006T=0.807C=0.193
1000GenomesGlobalStudy-wide5008T=0.910C=0.090
1000GenomesSouth AsianSub978T=0.860C=0.140
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.838C=0.162
The Genome Aggregation DatabaseAfricanSub8724T=0.948C=0.052
The Genome Aggregation DatabaseAmericanSub838T=0.900C=0.100
The Genome Aggregation DatabaseEast AsianSub1620T=0.984C=0.016
The Genome Aggregation DatabaseEuropeSub18480T=0.812C=0.187
The Genome Aggregation DatabaseGlobalStudy-wide29964T=0.863C=0.137
The Genome Aggregation DatabaseOtherSub302T=0.730C=0.270
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.888C=0.111
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.817C=0.183
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend
23953852Genome-wide association studies of maximum number of drinks.Pan YJ Psychiatr Res
22481050Genetic influences on craving for alcohol.Agrawal AAddict Behav

P-Value

SNP ID p-value Traits Study
rs117078970.0000241alcohol craving with or without dependence22481050
rs117078970.0000278nicotine dependence (smoking)22377092
rs117078970.0000311alcohol consumption23953852

eQTL of rs11707897 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 rs11707897 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 )
chr326109442611042E070-3584
chr326004432600933E081-13693
chr326189322619001E0814306
chr326191182619801E0814492
chr326199582620056E0815332
chr326206352620718E0816009
chr326215762621782E0816950
chr326218382622247E0817212
chr326238922624101E0819266
chr325989822599039E082-15587
chr326004432600933E082-13693
chr326189322619001E0824306
chr326191182619801E0824492
chr326206352620718E0826009
chr326215762621782E0826950