rs6552517

Homo sapiens
C>T
TENM3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0458 (13711/29906,GnomAD)
T=0491 (14306/29118,TOPMED)
C==0491 (2459/5008,1000G)
C==0384 (1481/3854,ALSPAC)
C==0361 (1340/3708,TWINSUK)
chr4:181655433 (GRCh38.p7) (4q34.3)
AD
GWASdb2
1   publication(s)
See rs on genome
22 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.181655433C>T
GRCh37.p13 chr 4NC_000004.11:g.182576586C>T

Gene: TENM3, teneurin transmembrane protein 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TENM3 transcriptNM_001080477.3:c.N/AGenic Upstream Transcript Variant
TENM3 transcript variant X1XM_017008385.1:c.N/AIntron Variant
TENM3 transcript variant X5XM_017008389.1:c.N/AIntron Variant
TENM3 transcript variant X6XM_017008390.1:c.N/AIntron Variant
TENM3 transcript variant X7XM_017008391.1:c.N/AIntron Variant
TENM3 transcript variant X8XM_017008392.1:c.N/AIntron Variant
TENM3 transcript variant X9XM_017008393.1:c.N/AIntron Variant
TENM3 transcript variant X10XM_017008394.1:c.N/AIntron Variant
TENM3 transcript variant X2XM_017008386.1:c.N/AGenic Upstream Transcript Variant
TENM3 transcript variant X3XM_017008387.1:c.N/AGenic Upstream Transcript Variant
TENM3 transcript variant X3XM_017008388.1:c.N/AGenic Upstream Transcript Variant
TENM3 transcript variant X11XM_017008395.1:c.N/AGenic Upstream Transcript Variant
TENM3 transcript variant X12XM_017008396.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.675T=0.325
1000GenomesAmericanSub694C=0.430T=0.570
1000GenomesEast AsianSub1008C=0.510T=0.490
1000GenomesEuropeSub1006C=0.414T=0.586
1000GenomesGlobalStudy-wide5008C=0.491T=0.509
1000GenomesSouth AsianSub978C=0.350T=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.384T=0.616
The Genome Aggregation DatabaseAfricanSub8688C=0.617T=0.383
The Genome Aggregation DatabaseAmericanSub836C=0.420T=0.580
The Genome Aggregation DatabaseEast AsianSub1614C=0.541T=0.459
The Genome Aggregation DatabaseEuropeSub18466C=0.379T=0.621
The Genome Aggregation DatabaseGlobalStudy-wide29906C=0.458T=0.541
The Genome Aggregation DatabaseOtherSub302C=0.410T=0.590
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.508T=0.491
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.361T=0.639
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
rs65525170.0003alcohol dependence20201924

eQTL of rs6552517 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 rs6552517 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 )
chr4182529419182529637E070-46949
chr4182529678182529759E070-46827
chr4182529872182529957E070-46629
chr4182529960182530136E070-46450
chr4182580950182581030E0704364
chr4182582301182582678E0705715
chr4182591715182591974E07115129
chr4182528455182528505E081-48081
chr4182529056182529114E081-47472
chr4182529419182529637E081-46949
chr4182529678182529759E081-46827
chr4182529872182529957E081-46629
chr4182529960182530136E081-46450
chr4182530278182530328E081-46258
chr4182530443182530534E081-46052
chr4182530620182530880E081-45706
chr4182532274182532337E081-44249
chr4182532406182532465E081-44121
chr4182532765182533002E081-43584
chr4182534437182534597E081-41989
chr4182530620182530880E082-45706
chr4182532274182532337E082-44249