rs1363204

Homo sapiens
T>A
TENM2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0108 (3241/29962,GnomAD)
A=0089 (2604/29118,TOPMED)
A=0177 (888/5008,1000G)
A=0106 (410/3854,ALSPAC)
A=0098 (362/3708,TWINSUK)
chr5:167893080 (GRCh38.p7) (5q34)
ND
GWASdb2
1   publication(s)
See rs on genome
3 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.167893080T>A
GRCh37.p13 chr 5NC_000005.9:g.167320085T>A

Gene: TENM2, teneurin transmembrane protein 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TENM2 transcript variant 2NM_001080428.2:c.N/AIntron Variant
TENM2 transcript variant 1NM_001122679.1:c.N/AIntron Variant
TENM2 transcript variant X3XM_005265950.2:c.N/AIntron Variant
TENM2 transcript variant X4XM_006714897.2:c.N/AIntron Variant
TENM2 transcript variant X6XM_011534604.2:c.N/AIntron Variant
TENM2 transcript variant X1XM_017009660.1:c.N/AIntron Variant
TENM2 transcript variant X2XM_017009661.1:c.N/AIntron Variant
TENM2 transcript variant X5XM_017009662.1:c.N/AIntron Variant
TENM2 transcript variant X7XM_017009663.1:c.N/AIntron Variant
TENM2 transcript variant X8XM_017009664.1:c.N/AIntron Variant
TENM2 transcript variant X9XM_017009665.1:c.N/AIntron Variant
TENM2 transcript variant X10XM_017009666.1:c.N/AIntron Variant
TENM2 transcript variant X11XM_017009667.1:c.N/AIntron Variant
TENM2 transcript variant X12XM_017009668.1:c.N/AIntron Variant
TENM2 transcript variant X13XM_017009669.1:c.N/AIntron Variant
TENM2 transcript variant X14XM_005265952.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.965A=0.035
1000GenomesAmericanSub694T=0.790A=0.210
1000GenomesEast AsianSub1008T=0.569A=0.431
1000GenomesEuropeSub1006T=0.907A=0.093
1000GenomesGlobalStudy-wide5008T=0.823A=0.177
1000GenomesSouth AsianSub978T=0.830A=0.170
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.894A=0.106
The Genome Aggregation DatabaseAfricanSub8728T=0.951A=0.049
The Genome Aggregation DatabaseAmericanSub838T=0.710A=0.290
The Genome Aggregation DatabaseEast AsianSub1610T=0.598A=0.402
The Genome Aggregation DatabaseEuropeSub18484T=0.897A=0.102
The Genome Aggregation DatabaseGlobalStudy-wide29962T=0.891A=0.108
The Genome Aggregation DatabaseOtherSub302T=0.920A=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.910A=0.089
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.902A=0.098
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs13632040.000989nicotine smoking19268276

eQTL of rs1363204 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 rs1363204 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 )
chr5167288262167288421E070-31664
chr5167288470167289124E070-30961
chr5167289178167289288E070-30797
chr5167289365167289665E070-30420
chr5167294427167294561E070-25524
chr5167288262167288421E071-31664
chr5167288262167288421E073-31664
chr5167345344167346137E07325259
chr5167288262167288421E081-31664
chr5167288470167289124E081-30961
chr5167289178167289288E081-30797
chr5167289365167289665E081-30420
chr5167291112167291166E081-28919
chr5167294427167294561E081-25524
chr5167323816167324134E0813731
chr5167324181167324417E0814096
chr5167326158167326356E0816073
chr5167326590167326875E0816505
chr5167339946167340631E08119861
chr5167342322167342637E08122237
chr5167343268167343740E08123183
chr5167343817167344037E08123732
chr5167345210167345294E08125125
chr5167345344167346137E08125259
chr5167346262167346414E08126177
chr5167346561167346691E08126476
chr5167288262167288421E082-31664
chr5167294427167294561E082-25524
chr5167323816167324134E0823731
chr5167339946167340631E08219861
chr5167345210167345294E08225125
chr5167345344167346137E08225259
chr5167346561167346691E08226476
chr5167360492167360661E08240407





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5167361529167361840E06841444
chr5167361529167361840E07241444
chr5167361529167361840E07341444