rs10279700

Homo sapiens
T>C
CNTNAP2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0163 (4905/29956,GnomAD)
C=0162 (4724/29118,TOPMED)
C=0340 (1704/5008,1000G)
C=0106 (410/3854,ALSPAC)
C=0106 (394/3708,TWINSUK)
chr7:147271203 (GRCh38.p7) (7q35)
AD
GWASdb2
1   publication(s)
See rs on genome
22 Enhancers around
6 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.147271203T>C
GRCh37.p13 chr 7NC_000007.13:g.146968295T>C
CNTNAP2 RefSeqGeneNG_007092.2:g.1159843T>C

Gene: CNTNAP2, contactin associated protein-like 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CNTNAP2 transcriptNM_014141.5:c.N/AIntron Variant
CNTNAP2 transcript variant X1XM_017011950.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.821C=0.179
1000GenomesAmericanSub694T=0.700C=0.300
1000GenomesEast AsianSub1008T=0.225C=0.775
1000GenomesEuropeSub1006T=0.868C=0.132
1000GenomesGlobalStudy-wide5008T=0.660C=0.340
1000GenomesSouth AsianSub978T=0.650C=0.350
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.894C=0.106
The Genome Aggregation DatabaseAfricanSub8714T=0.835C=0.165
The Genome Aggregation DatabaseAmericanSub836T=0.690C=0.310
The Genome Aggregation DatabaseEast AsianSub1616T=0.248C=0.752
The Genome Aggregation DatabaseEuropeSub18488T=0.894C=0.105
The Genome Aggregation DatabaseGlobalStudy-wide29956T=0.836C=0.163
The Genome Aggregation DatabaseOtherSub302T=0.850C=0.150
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.837C=0.162
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.894C=0.106
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs102797004.08E-05alcohol dependence21314694

eQTL of rs10279700 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 rs10279700 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 )
chr7146978225146978279E0679930
chr7146932861146933381E068-34914
chr7146973944146974142E0685649
chr7146974197146974247E0685902
chr7146974366146974474E0686071
chr7146978225146978279E0689930
chr7146978742146978796E06810447
chr7146979091146979141E06810796
chr7146932861146933381E069-34914
chr7146974197146974247E0695902
chr7147008443147008493E07140148
chr7147008580147008727E07140285
chr7147008731147008783E07140436
chr7146932861146933381E072-34914
chr7146932861146933381E073-34914
chr7146973944146974142E0815649
chr7146974197146974247E0815902
chr7146974366146974474E0816071
chr7146973616146973666E0825321
chr7146973944146974142E0825649
chr7146974197146974247E0825902
chr7146974366146974474E0826071








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr7146977042146977506E0678747
chr7146977042146977506E0688747
chr7146977042146977506E0698747
chr7146977042146977506E0718747
chr7146977042146977506E0728747
chr7146977042146977506E0748747