rs16849613

Homo sapiens
T>A
CLSTN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0096 (2897/29924,GnomAD)
A=0117 (3412/29118,TOPMED)
A=0093 (467/5008,1000G)
A=0083 (319/3854,ALSPAC)
A=0083 (306/3708,TWINSUK)
chr3:139979746 (GRCh38.p7) (3q23)
ND
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.139979746T>A
GRCh37.p13 chr 3NC_000003.11:g.139698588T>A

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/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.790A=0.210
1000GenomesAmericanSub694T=0.940A=0.060
1000GenomesEast AsianSub1008T=0.998A=0.002
1000GenomesEuropeSub1006T=0.914A=0.086
1000GenomesGlobalStudy-wide5008T=0.907A=0.093
1000GenomesSouth AsianSub978T=0.940A=0.060
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.917A=0.083
The Genome Aggregation DatabaseAfricanSub8700T=0.832A=0.168
The Genome Aggregation DatabaseAmericanSub834T=0.960A=0.040
The Genome Aggregation DatabaseEast AsianSub1622T=1.000A=0.000
The Genome Aggregation DatabaseEuropeSub18466T=0.925A=0.074
The Genome Aggregation DatabaseGlobalStudy-wide29924T=0.903A=0.096
The Genome Aggregation DatabaseOtherSub302T=0.930A=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.882A=0.117
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.917A=0.083
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
rs168496130.00015nicotine smoking19268276

eQTL of rs16849613 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 rs16849613 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 )
chr3139656646139656807E067-41781
chr3139657084139657274E067-41314
chr3139726861139727082E06728273
chr3139727332139727697E06728744
chr3139731913139732568E06733325
chr3139740201139740446E06741613
chr3139741253139741507E06742665
chr3139742125139742241E06743537
chr3139742446139742818E06743858
chr3139657084139657274E068-41314
chr3139727332139727697E06828744
chr3139738831139739135E06840243
chr3139740201139740446E06841613
chr3139741253139741507E06842665
chr3139742125139742241E06843537
chr3139742446139742818E06843858
chr3139726163139726236E06927575
chr3139726861139727082E06928273
chr3139727332139727697E06928744
chr3139740026139740099E06941438
chr3139740201139740446E06941613
chr3139741253139741507E06942665
chr3139742125139742241E06943537
chr3139742446139742818E06943858
chr3139725303139725403E07026715
chr3139725923139725977E07027335
chr3139726024139726099E07027436
chr3139726163139726236E07027575
chr3139726861139727082E07028273
chr3139727332139727697E07028744
chr3139739723139739778E07041135
chr3139741253139741507E07042665
chr3139742125139742241E07043537
chr3139742446139742818E07043858
chr3139726861139727082E07128273
chr3139727332139727697E07128744
chr3139731913139732568E07133325
chr3139738579139738636E07139991
chr3139738831139739135E07140243
chr3139739723139739778E07141135
chr3139740026139740099E07141438
chr3139740201139740446E07141613
chr3139741253139741507E07142665
chr3139742125139742241E07143537
chr3139742446139742818E07143858
chr3139725303139725403E07226715
chr3139725923139725977E07227335
chr3139726024139726099E07227436
chr3139726163139726236E07227575
chr3139726861139727082E07228273
chr3139727332139727697E07228744
chr3139731913139732568E07233325
chr3139734044139734132E07235456
chr3139739723139739778E07241135
chr3139740026139740099E07241438
chr3139740201139740446E07241613
chr3139741253139741507E07242665
chr3139742125139742241E07243537
chr3139742446139742818E07243858
chr3139731913139732568E07333325
chr3139740026139740099E07341438
chr3139740201139740446E07341613
chr3139741253139741507E07342665
chr3139742125139742241E07343537
chr3139742446139742818E07343858
chr3139726861139727082E07428273
chr3139727332139727697E07428744
chr3139734044139734132E07435456
chr3139738831139739135E07440243
chr3139739723139739778E07441135
chr3139740026139740099E07441438
chr3139740201139740446E07441613
chr3139741253139741507E07442665
chr3139742125139742241E07443537
chr3139742446139742818E07443858
chr3139731913139732568E08133325
chr3139735035139735096E08136447
chr3139738342139738485E08139754
chr3139738579139738636E08139991
chr3139741253139741507E08142665
chr3139742125139742241E08143537
chr3139742446139742818E08143858
chr3139694587139694693E082-3895
chr3139694704139694754E082-3834
chr3139694916139695018E082-3570
chr3139695207139695269E082-3319
chr3139726861139727082E08228273
chr3139727332139727697E08228744
chr3139731913139732568E08233325
chr3139741253139741507E08242665
chr3139742125139742241E08243537
chr3139742446139742818E08243858










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3139653394139655357E067-43231
chr3139655390139655551E067-43037
chr3139653258139653341E068-45247
chr3139653394139655357E068-43231
chr3139655390139655551E068-43037
chr3139653258139653341E069-45247
chr3139653394139655357E069-43231
chr3139653394139655357E071-43231
chr3139653258139653341E072-45247
chr3139653394139655357E072-43231
chr3139655390139655551E072-43037
chr3139653394139655357E073-43231
chr3139653394139655357E074-43231
chr3139655390139655551E074-43037
chr3139653394139655357E082-43231