rs2157588

Homo sapiens
C>T
TNN : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0384 (11523/29940,GnomAD)
T=0334 (9734/29118,TOPMED)
T=0269 (1349/5008,1000G)
T=0460 (1773/3854,ALSPAC)
T=0486 (1803/3708,TWINSUK)
chr1:175138690 (GRCh38.p7) (1q25.1)
AD
GWASdb2
2   publication(s)
See rs on genome
21 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.175138690C>T
GRCh37.p13 chr 1NC_000001.10:g.175107826C>T

Gene: TNN, tenascin N(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TNN transcriptNM_022093.1:c.N/AIntron Variant
TNN transcript variant X1XM_017002048.1:c.N/AIntron Variant
TNN transcript variant X2XM_017002049.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.741T=0.259
1000GenomesAmericanSub694C=0.700T=0.300
1000GenomesEast AsianSub1008C=0.914T=0.086
1000GenomesEuropeSub1006C=0.536T=0.464
1000GenomesGlobalStudy-wide5008C=0.731T=0.269
1000GenomesSouth AsianSub978C=0.750T=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.540T=0.460
The Genome Aggregation DatabaseAfricanSub8708C=0.726T=0.274
The Genome Aggregation DatabaseAmericanSub836C=0.730T=0.270
The Genome Aggregation DatabaseEast AsianSub1620C=0.920T=0.080
The Genome Aggregation DatabaseEuropeSub18474C=0.529T=0.470
The Genome Aggregation DatabaseGlobalStudy-wide29940C=0.615T=0.384
The Genome Aggregation DatabaseOtherSub302C=0.680T=0.320
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.665T=0.334
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.514T=0.486
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology

P-Value

SNP ID p-value Traits Study
rs21575887.16E-05alcohol dependence21703634

eQTL of rs2157588 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 rs2157588 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 )
chr1175127262175127638E06719436
chr1175127726175127793E06719900
chr1175121212175121706E06913386
chr1175138495175138718E06930669
chr1175117508175117593E0709682
chr1175131566175131616E07023740
chr1175131702175131793E07023876
chr1175131845175132044E07024019
chr1175132208175132358E07024382
chr1175121212175121706E07213386
chr1175115170175115364E0817344
chr1175115429175115500E0817603
chr1175115737175116333E0817911
chr1175116438175116534E0818612
chr1175116763175117071E0818937
chr1175117325175117401E0819499
chr1175117508175117593E0819682
chr1175120951175121040E08113125
chr1175121212175121706E08113386
chr1175127262175127638E08219436
chr1175127726175127793E08219900