rs17479252

Homo sapiens
C>T
TSPAN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0335 (10030/29906,GnomAD)
T=0313 (9133/29118,TOPMED)
T=0290 (1451/5008,1000G)
T=0414 (1597/3854,ALSPAC)
T=0415 (1539/3708,TWINSUK)
chr1:115079239 (GRCh38.p7) (1p13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
5 Enhancers around
12 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.115079239C>T
GRCh37.p13 chr 1NC_000001.10:g.115621860C>T

Gene: TSPAN2, tetraspanin 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TSPAN2 transcript variant 2NM_001308315.1:c.N/AIntron Variant
TSPAN2 transcript variant 3NM_001308316.1:c.N/AIntron Variant
TSPAN2 transcript variant 1NM_005725.5:c.N/AIntron Variant
TSPAN2 transcript variant X1XM_016999996.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.844T=0.156
1000GenomesAmericanSub694C=0.700T=0.300
1000GenomesEast AsianSub1008C=0.750T=0.250
1000GenomesEuropeSub1006C=0.579T=0.421
1000GenomesGlobalStudy-wide5008C=0.710T=0.290
1000GenomesSouth AsianSub978C=0.630T=0.370
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.586T=0.414
The Genome Aggregation DatabaseAfricanSub8702C=0.816T=0.184
The Genome Aggregation DatabaseAmericanSub836C=0.690T=0.310
The Genome Aggregation DatabaseEast AsianSub1612C=0.703T=0.297
The Genome Aggregation DatabaseEuropeSub18454C=0.590T=0.409
The Genome Aggregation DatabaseGlobalStudy-wide29906C=0.664T=0.335
The Genome Aggregation DatabaseOtherSub302C=0.560T=0.440
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.686T=0.313
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.585T=0.415
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
rs174792520.000995alcohol dependence21314694

eQTL of rs17479252 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:115621860TSPAN2ENSG00000134198.5C>T5.2445e-13-10261Cerebellum

meQTL of rs17479252 in Fetal Brain

Probe ID Position Gene beta p-value
cg09811183chr1:115631515TSPAN20.04209659214373342.3773e-14

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 )
chr1115626112115626259E0684252
chr1115626562115626666E0684702
chr1115598948115599450E072-22410
chr1115628351115628391E0816491
chr1115630740115631257E0818880



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1115631361115633456E0679501
chr1115631361115633456E0689501
chr1115641370115642665E06819510
chr1115631361115633456E0699501
chr1115641370115642665E06919510
chr1115631361115633456E0709501
chr1115631361115633456E0719501
chr1115641370115642665E07119510
chr1115631361115633456E0729501
chr1115631361115633456E0739501
chr1115631361115633456E0749501
chr1115631361115633456E0829501