rs2288158

Homo sapiens
T>G
NCAM1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0176 (17042/96532,ExAC)
G=0136 (4090/29966,GnomAD)
G=0136 (3965/29118,TOPMED)
T==0129 (1555/11978,GO-ESP)
G=0159 (794/5008,1000G)
G=0148 (570/3854,ALSPAC)
G=0127 (470/3708,TWINSUK)
chr11:113262954 (GRCh38.p7) (11q23.2)
ND
GWASdb2
1   publication(s)
See rs on genome
149 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.113262954T>G
GRCh37.p13 chr 11 fix patch HG306_PATCHNW_003871078.1:g.445680T>G
NCAM1 RefSeqGeneNG_032036.1:g.306708T>G
GRCh37.p13 chr 11NC_000011.9:g.113133676T>G

Gene: NCAM1, neural cell adhesion molecule 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NCAM1 transcript variant 1NM_000615.6:c.N/AIntron Variant
NCAM1 transcript variant 5NM_001242607.1:c.N/AIntron Variant
NCAM1 transcript variant 2NM_181351.4:c.N/AIntron Variant
NCAM1 transcript variant 3NM_001076682.3:c.N/A3 Prime UTR Variant
NCAM1 transcript variant 4NM_001242608.1:c.N/A3 Prime UTR Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.907G=0.093
1000GenomesAmericanSub694T=0.890G=0.110
1000GenomesEast AsianSub1008T=0.700G=0.300
1000GenomesEuropeSub1006T=0.885G=0.115
1000GenomesGlobalStudy-wide5008T=0.841G=0.159
1000GenomesSouth AsianSub978T=0.820G=0.180
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.852G=0.148
The Exome Aggregation ConsortiumAmericanSub16280T=0.862G=0.137
The Exome Aggregation ConsortiumAsianSub20676T=0.755G=0.244
The Exome Aggregation ConsortiumEuropeSub58820T=0.836G=0.163
The Exome Aggregation ConsortiumGlobalStudy-wide96532T=0.823G=0.176
The Exome Aggregation ConsortiumOtherSub756T=0.840G=0.160
The Genome Aggregation DatabaseAfricanSub8722T=0.895G=0.105
The Genome Aggregation DatabaseAmericanSub836T=0.910G=0.090
The Genome Aggregation DatabaseEast AsianSub1614T=0.693G=0.307
The Genome Aggregation DatabaseEuropeSub18492T=0.862G=0.137
The Genome Aggregation DatabaseGlobalStudy-wide29966T=0.863G=0.136
The Genome Aggregation DatabaseOtherSub302T=0.810G=0.190
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.863G=0.136
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.873G=0.127
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs22881588.98E-05nicotine dependence (smoking)22377092

eQTL of rs2288158 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 rs2288158 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 )
chr11449140449294E0673460
chr11451917451975E0676237
chr11470287470555E06724607
chr11476036476111E06730356
chr11476189476245E06730509
chr11476501476590E06730821
chr11476777476837E06731097
chr11477085477135E06731405
chr11477159477329E06731479
chr11477457477585E06731777
chr11479158479332E06733478
chr11479455479574E06733775
chr11494512494631E06748832
chr11494697495232E06749017
chr11495269495499E06749589
chr11495547495630E06749867
chr11443545443981E068-1699
chr11451917451975E0686237
chr11468203468961E06822523
chr11468994469034E06823314
chr11494370494468E06848690
chr11494512494631E06848832
chr11494697495232E06849017
chr11495269495499E06849589
chr11495547495630E06849867
chr11405412405591E069-40089
chr11451917451975E0696237
chr11452027452531E0696347
chr11452536452752E0696856
chr11476036476111E06930356
chr11476189476245E06930509
chr11476501476590E06930821
chr11476777476837E06931097
chr11477085477135E06931405
chr11477159477329E06931479
chr11477457477585E06931777
chr11477755477862E06932075
chr11479158479332E06933478
chr11479455479574E06933775
chr11493906494047E06948226
chr11494058494130E06948378
chr11494241494313E06948561
chr11494370494468E06948690
chr11494512494631E06948832
chr11494697495232E06949017
chr11495269495499E06949589
chr11495547495630E06949867
chr11449140449294E0703460
chr11452027452531E0706347
chr11452536452752E0706856
chr11468203468961E07022523
chr11451917451975E0716237
chr11452027452531E0716347
chr11468203468961E07122523
chr11476501476590E07130821
chr11476777476837E07131097
chr11477085477135E07131405
chr11477159477329E07131479
chr11477457477585E07131777
chr11478958479092E07133278
chr11479158479332E07133478
chr11479455479574E07133775
chr11493906494047E07148226
chr11494058494130E07148378
chr11494241494313E07148561
chr11494370494468E07148690
chr11494512494631E07148832
chr11494697495232E07149017
chr11495269495499E07149589
chr11495547495630E07149867
chr11405211405360E072-40320
chr11405412405591E072-40089
chr11449140449294E0723460
chr11451917451975E0726237
chr11452027452531E0726347
chr11452536452752E0726856
chr11468203468961E07222523
chr11468994469034E07223314
chr11469139469267E07223459
chr11472227472287E07226547
chr11472344472499E07226664
chr11476189476245E07230509
chr11476501476590E07230821
chr11476777476837E07231097
chr11477085477135E07231405
chr11477159477329E07231479
chr11477457477585E07231777
chr11477755477862E07232075
chr11478958479092E07233278
chr11479158479332E07233478
chr11479455479574E07233775
chr11483789483839E07238109
chr11488166488295E07242486
chr11488364488445E07242684
chr11488497488547E07242817
chr11488609488670E07242929
chr11489126489403E07243446
chr11489467489517E07243787
chr11489720489770E07244040
chr11490602490804E07244922
chr11490808490965E07245128
chr11491061491286E07245381
chr11493906494047E07248226
chr11494058494130E07248378
chr11494241494313E07248561
chr11494370494468E07248690
chr11494512494631E07248832
chr11494697495232E07249017
chr11495269495499E07249589
chr11495547495630E07249867
chr11476777476837E07331097
chr11477085477135E07331405
chr11477159477329E07331479
chr11477457477585E07331777
chr11479158479332E07333478
chr11479455479574E07333775
chr11494370494468E07348690
chr11494512494631E07348832
chr11494697495232E07349017
chr11495269495499E07349589
chr11495547495630E07349867
chr11449140449294E0743460
chr11451917451975E0746237
chr11468203468961E07422523
chr11468994469034E07423314
chr11469139469267E07423459
chr11469367469461E07423687
chr11476501476590E07430821
chr11476777476837E07431097
chr11477085477135E07431405
chr11477159477329E07431479
chr11477457477585E07431777
chr11478958479092E07433278
chr11479158479332E07433478
chr11479455479574E07433775
chr11493906494047E07448226
chr11494058494130E07448378
chr11494241494313E07448561
chr11494370494468E07448690
chr11494512494631E07448832
chr11494697495232E07449017
chr11495269495499E07449589
chr11495547495630E07449867
chr11449140449294E0813460
chr11451917451975E0816237
chr11452027452531E0816347
chr11451917451975E0826237
chr11452027452531E0826347
chr11452536452752E0826856










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11447922449037E0672242
chr11449822451623E0674142
chr11414368418062E068-27618
chr11447922449037E0682242
chr11449822451623E0684142
chr11447922449037E0692242
chr11449822451623E0694142
chr11447922449037E0702242
chr11449822451623E0704142
chr11447922449037E0712242
chr11449822451623E0714142
chr11447922449037E0722242
chr11449822451623E0724142
chr11447922449037E0732242
chr11449822451623E0734142
chr11447922449037E0742242
chr11449822451623E0744142
chr11449822451623E0814142
chr11447922449037E0822242
chr11449822451623E0824142