rs6798469

Homo sapiens
C>T
CLSTN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0009 (277/29988,GnomAD)
C==0008 (253/29118,TOPMED)
C==0006 (31/5008,1000G)
C==0023 (88/3854,ALSPAC)
C==0019 (72/3708,TWINSUK)
chr3:140182692 (GRCh38.p7) (3q23)
ND
GWASdb2
1   publication(s)
See rs on genome
92 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.140182692C>T
GRCh37.p13 chr 3NC_000003.11:g.139901534C>T

Gene: CLSTN2, calsyntenin 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CLSTN2 transcriptNM_022131.2:c.N/AIntron Variant
CLSTN2 transcript variant X1XM_017007022.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.001T=0.999
1000GenomesAmericanSub694C=0.000T=1.000
1000GenomesEast AsianSub1008C=0.000T=1.000
1000GenomesEuropeSub1006C=0.016T=0.984
1000GenomesGlobalStudy-wide5008C=0.006T=0.994
1000GenomesSouth AsianSub978C=0.010T=0.990
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.023T=0.977
The Genome Aggregation DatabaseAfricanSub8728C=0.004T=0.996
The Genome Aggregation DatabaseAmericanSub838C=0.010T=0.990
The Genome Aggregation DatabaseEast AsianSub1616C=0.000T=1.000
The Genome Aggregation DatabaseEuropeSub18504C=0.012T=0.987
The Genome Aggregation DatabaseGlobalStudy-wide29988C=0.009T=0.990
The Genome Aggregation DatabaseOtherSub302C=0.000T=1.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.008T=0.991
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.019T=0.981
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
rs67984690.000991nicotine smoking19268276

eQTL of rs6798469 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 rs6798469 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 )
chr3139861891139862194E067-39340
chr3139862383139863008E067-38526
chr3139905127139905695E0673593
chr3139905988139906087E0674454
chr3139906259139906426E0674725
chr3139917224139917367E06715690
chr3139917975139918030E06716441
chr3139918647139918757E06717113
chr3139918831139918907E06717297
chr3139919014139919064E06717480
chr3139919248139919306E06717714
chr3139917224139917367E06815690
chr3139917975139918030E06816441
chr3139862383139863008E069-38526
chr3139885534139885584E069-15950
chr3139885816139886054E069-15480
chr3139905988139906087E0694454
chr3139906259139906426E0694725
chr3139917224139917367E06915690
chr3139917975139918030E06916441
chr3139918647139918757E06917113
chr3139918831139918907E06917297
chr3139919014139919064E06917480
chr3139919248139919306E06917714
chr3139861891139862194E070-39340
chr3139865780139865883E070-35651
chr3139872077139872287E070-29247
chr3139905127139905695E0703593
chr3139905988139906087E0704454
chr3139906259139906426E0704725
chr3139906558139906958E0705024
chr3139907026139907077E0705492
chr3139907287139907436E0705753
chr3139917224139917367E07015690
chr3139918647139918757E07017113
chr3139918831139918907E07017297
chr3139919014139919064E07017480
chr3139919248139919306E07017714
chr3139922391139922450E07020857
chr3139922507139922671E07020973
chr3139862383139863008E071-38526
chr3139885534139885584E071-15950
chr3139885816139886054E071-15480
chr3139905127139905695E0713593
chr3139905988139906087E0714454
chr3139906259139906426E0714725
chr3139906558139906958E0715024
chr3139917224139917367E07115690
chr3139917975139918030E07116441
chr3139862383139863008E072-38526
chr3139885816139886054E072-15480
chr3139905127139905695E0723593
chr3139905988139906087E0724454
chr3139906259139906426E0724725
chr3139917224139917367E07215690
chr3139917975139918030E07216441
chr3139918647139918757E07217113
chr3139918831139918907E07217297
chr3139919014139919064E07217480
chr3139919248139919306E07217714
chr3139905127139905695E0733593
chr3139905988139906087E0734454
chr3139906259139906426E0734725
chr3139917224139917367E07315690
chr3139917975139918030E07316441
chr3139862383139863008E074-38526
chr3139885534139885584E074-15950
chr3139885816139886054E074-15480
chr3139905127139905695E0743593
chr3139905988139906087E0744454
chr3139906259139906426E0744725
chr3139906558139906958E0745024
chr3139907026139907077E0745492
chr3139917224139917367E07415690
chr3139917975139918030E07416441
chr3139918647139918757E07417113
chr3139918831139918907E07417297
chr3139919014139919064E07417480
chr3139919248139919306E07417714
chr3139861891139862194E081-39340
chr3139862383139863008E081-38526
chr3139864501139864784E081-36750
chr3139865780139865883E081-35651
chr3139884118139884306E081-17228
chr3139884723139884947E081-16587
chr3139905988139906087E0814454
chr3139861891139862194E082-39340
chr3139862383139863008E082-38526
chr3139922391139922450E08220857
chr3139922507139922671E08220973
chr3139922842139923018E08221308
chr3139923131139923780E08221597