rs11102878

Homo sapiens
T>C
TSPAN2 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0419 (12236/29194,GnomAD)
C=0384 (11183/29118,TOPMED)
C=0373 (1869/5008,1000G)
C=0499 (1925/3854,ALSPAC)
T==0494 (1831/3708,TWINSUK)
chr1:115048377 (GRCh38.p7) (1p13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
5 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.115048377T>C
GRCh37.p13 chr 1NC_000001.10:g.115590998T>C

Gene: TSPAN2, tetraspanin 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TSPAN2 transcript variant 1NM_005725.5:c.N/A3 Prime UTR Variant
TSPAN2 transcript variant 2NM_001308315.1:c.N/A3 Prime UTR Variant
TSPAN2 transcript variant 3NM_001308316.1:c.N/A3 Prime UTR Variant
TSPAN2 transcript variant X1XM_016999996.1:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.803C=0.197
1000GenomesAmericanSub694T=0.600C=0.400
1000GenomesEast AsianSub1008T=0.472C=0.528
1000GenomesEuropeSub1006T=0.524C=0.476
1000GenomesGlobalStudy-wide5008T=0.627C=0.373
1000GenomesSouth AsianSub978T=0.670C=0.330
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.501C=0.499
The Genome Aggregation DatabaseAfricanSub8596T=0.762C=0.238
The Genome Aggregation DatabaseAmericanSub730T=0.580C=0.420
The Genome Aggregation DatabaseEast AsianSub1608T=0.503C=0.497
The Genome Aggregation DatabaseEuropeSub17960T=0.503C=0.496
The Genome Aggregation DatabaseGlobalStudy-wide29194T=0.580C=0.419
The Genome Aggregation DatabaseOtherSub300T=0.440C=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.615C=0.384
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.494C=0.506
PMID Title Author Journal
23953852Genome-wide association studies of maximum number of drinks.Pan YJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs111028786.89E-05alcohol consumption23953852

eQTL of rs11102878 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:115590998TSPAN2ENSG00000134198.5T>C5.2445e-13-41123Cerebellum

meQTL of rs11102878 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 )
chr1115626112115626259E06835114
chr1115626562115626666E06835564
chr1115598948115599450E0727950
chr1115628351115628391E08137353
chr1115630740115631257E08139742



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1115631361115633456E06740363
chr1115631361115633456E06840363
chr1115631361115633456E06940363
chr1115631361115633456E07040363
chr1115631361115633456E07140363
chr1115631361115633456E07240363
chr1115631361115633456E07340363
chr1115631361115633456E07440363
chr1115631361115633456E08240363