rs2728055

Homo sapiens
C>T
CNTN4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0377 (11273/29892,GnomAD)
C==0378 (11026/29118,TOPMED)
C==0438 (2196/5008,1000G)
C==0366 (1409/3854,ALSPAC)
C==0350 (1296/3708,TWINSUK)
chr3:2574606 (GRCh38.p7) (3p26.3)
AD
GWASdb2
1   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.2574606C>T
GRCh37.p13 chr 3NC_000003.11:g.2616290C>T
CNTN4 RefSeqGeneNG_012827.1:g.479044C>T

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
1000GenomesAfricanSub1322C=0.430T=0.570
1000GenomesAmericanSub694C=0.370T=0.630
1000GenomesEast AsianSub1008C=0.497T=0.503
1000GenomesEuropeSub1006C=0.331T=0.669
1000GenomesGlobalStudy-wide5008C=0.438T=0.562
1000GenomesSouth AsianSub978C=0.550T=0.450
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.366T=0.634
The Genome Aggregation DatabaseAfricanSub8692C=0.420T=0.580
The Genome Aggregation DatabaseAmericanSub836C=0.330T=0.670
The Genome Aggregation DatabaseEast AsianSub1610C=0.473T=0.527
The Genome Aggregation DatabaseEuropeSub18452C=0.352T=0.648
The Genome Aggregation DatabaseGlobalStudy-wide29892C=0.377T=0.622
The Genome Aggregation DatabaseOtherSub302C=0.280T=0.720
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.378T=0.621
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.350T=0.650
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
rs27280550.00017alcohol dependence20201924

eQTL of rs2728055 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 rs2728055 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 )
chr326109442611042E070-5248
chr326004432600933E081-15357
chr326189322619001E0812642
chr326191182619801E0812828
chr326199582620056E0813668
chr326206352620718E0814345
chr326215762621782E0815286
chr326218382622247E0815548
chr326238922624101E0817602
chr325989822599039E082-17251
chr326004432600933E082-15357
chr326189322619001E0822642
chr326191182619801E0822828
chr326206352620718E0824345
chr326215762621782E0825286