rs1197701

Homo sapiens
T>C / T>G
SPTBN5 : 2KB Upstream Variant
LOC105370792 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0290 (8687/29890,GnomAD)
C=0326 (9506/29118,TOPMED)
C=0329 (4352/13214,ExAC)
C=0315 (1580/5008,1000G)
C=0255 (981/3854,ALSPAC)
C=0265 (983/3708,TWINSUK)
chr15:41895294 (GRCh38.p7) (15q15.1)
ND
GWASdb2
1   publication(s)
See rs on genome
148 Enhancers around
11 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.41895294T>C
GRCh38.p7 chr 15NC_000015.10:g.41895294T>G
GRCh37.p13 chr 15NC_000015.9:g.42187492T>C
GRCh37.p13 chr 15NC_000015.9:g.42187492T>G

Gene: SPTBN5, spectrin beta, non-erythrocytic 5(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
SPTBN5 transcriptNM_016642.3:c.N/AUpstream Transcript Variant
SPTBN5 transcript variant X1XM_017022299.1:c.N/AUpstream Transcript Variant
SPTBN5 transcript variant X2XM_017022300.1:c.N/AUpstream Transcript Variant
SPTBN5 transcript variant X8XM_017022303.1:c.N/AUpstream Transcript Variant
SPTBN5 transcript variant X9XM_017022304.1:c.N/AUpstream Transcript Variant
SPTBN5 transcript variant X11XM_017022305.1:c.N/AUpstream Transcript Variant
SPTBN5 transcript variant X3XM_017022301.1:c.N/AN/A
SPTBN5 transcript variant X4XM_017022302.1:c.N/AN/A
SPTBN5 transcript variant X5XR_001751302.1:n.N/AUpstream Transcript Variant
SPTBN5 transcript variant X6XR_001751303.1:n.N/AUpstream Transcript Variant
SPTBN5 transcript variant X7XR_001751304.1:n.N/AUpstream Transcript Variant
SPTBN5 transcript variant X10XR_001751305.1:n.N/AUpstream Transcript Variant

Gene: LOC105370792, uncharacterized LOC105370792(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105370792 transcriptNR_135681.1:n.370T>CT>CNon Coding Transcript Variant
LOC105370792 transcriptNR_135681.1:n.370T>GT>GNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.628C=0.372
1000GenomesAmericanSub694T=0.750C=0.250
1000GenomesEast AsianSub1008T=0.693C=0.307
1000GenomesEuropeSub1006T=0.717C=0.283
1000GenomesGlobalStudy-wide5008T=0.685C=0.315
1000GenomesSouth AsianSub978T=0.670C=0.330
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.745C=0.255
The Exome Aggregation ConsortiumAmericanSub756T=0.640C=0.360
The Exome Aggregation ConsortiumAsianSub7156T=0.659C=0.341
The Exome Aggregation ConsortiumEuropeSub5130T=0.692C=0.308
The Exome Aggregation ConsortiumGlobalStudy-wide13214T=0.670C=0.329
The Exome Aggregation ConsortiumOtherSub172T=0.650C=0.350
The Genome Aggregation DatabaseAfricanSub8686T=0.631G=0.000
The Genome Aggregation DatabaseAmericanSub836T=0.740G=0.00,
The Genome Aggregation DatabaseEast AsianSub1612T=0.663G=0.000
The Genome Aggregation DatabaseEuropeSub18454T=0.750G=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29890T=0.709G=0.000
The Genome Aggregation DatabaseOtherSub302T=0.610G=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.673C=0.326
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.735C=0.265
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
rs11977018.46E-05nicotine dependence (smoking)22377092

eQTL of rs1197701 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:42187492MAPKBP1ENSG00000137802.9T>C1.6567e-7120860Cerebellum
Chr15:42187492SPTBN5ENSG00000137877.8T>C2.3126e-165089Cerebellum
Chr15:42187492RP11-23P13.6ENSG00000174171.4T>C1.9445e-142501Cerebellum
Chr15:42187492RP11-23P13.7ENSG00000272003.1T>C1.1554e-12-1539Cerebellum
Chr15:42187492EHD4ENSG00000103966.5T>C9.1353e-17-77284Cerebellum
Chr15:42187492SPTBN5ENSG00000137877.8T>C5.1172e-95089Cerebellar_Hemisphere
Chr15:42187492RP11-23P13.6ENSG00000174171.4T>C1.1246e-102501Cerebellar_Hemisphere
Chr15:42187492RP11-23P13.7ENSG00000272003.1T>C5.4113e-10-1539Cerebellar_Hemisphere
Chr15:42187492EHD4ENSG00000103966.5T>C4.3181e-11-77284Cerebellar_Hemisphere

meQTL of rs1197701 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 )
chr154219640142196530E067-25860
chr154219653542197728E067-24662
chr154220524542205538E067-16852
chr154220560742205740E067-16650
chr154220608042206307E067-16083
chr154220635242206964E067-15426
chr154220730442207413E067-14977
chr154220838642208775E067-13615
chr154220975142210616E067-11774
chr154218613342186413E068-35977
chr154219653542197728E068-24662
chr154220730442207413E068-14977
chr154220757742207700E068-14690
chr154220770142207844E068-14546
chr154220788942207995E068-14395
chr154220838642208775E068-13615
chr154220975142210616E068-11774
chr154221335942213718E068-8672
chr154221371942214354E068-8036
chr154222086642221907E068-483
chr154222227642223283E0680
chr154223041242230535E0688022
chr154225939842259602E06837008
chr154225974242259865E06837352
chr154217517442176015E069-46375
chr154218646242187988E069-34402
chr154220524542205538E069-16852
chr154220560742205740E069-16650
chr154220757742207700E069-14690
chr154220770142207844E069-14546
chr154220788942207995E069-14395
chr154220975142210616E069-11774
chr154221371942214354E069-8036
chr154222086642221907E069-483
chr154222884942230116E0696459
chr154224368442243922E06921294
chr154224415142244205E06921761
chr154224420642244350E06921816
chr154224438742244442E06921997
chr154225988442260391E06937494
chr154226040142260594E06938011
chr154226071742260767E06938327
chr154217517442176015E071-46375
chr154218646242187988E071-34402
chr154219640142196530E071-25860
chr154219653542197728E071-24662
chr154220496242205103E071-17287
chr154220511442205198E071-17192
chr154220524542205538E071-16852
chr154220560742205740E071-16650
chr154220608042206307E071-16083
chr154220635242206964E071-15426
chr154220730442207413E071-14977
chr154220757742207700E071-14690
chr154220770142207844E071-14546
chr154220788942207995E071-14395
chr154220838642208775E071-13615
chr154220975142210616E071-11774
chr154221061742211458E071-10932
chr154221148442212128E071-10262
chr154221371942214354E071-8036
chr154222086642221907E071-483
chr154222194542222112E071-278
chr154222227642223283E0710
chr154222677742227594E0714387
chr154222778842227988E0715398
chr154222884942230116E0716459
chr154224331342243363E07120923
chr154224338942243433E07120999
chr154224351142243568E07121121
chr154224360842243681E07121218
chr154224368442243922E07121294
chr154224415142244205E07121761
chr154224420642244350E07121816
chr154224438742244442E07121997
chr154224451242244628E07122122
chr154224471742244794E07122327
chr154225816642258667E07135776
chr154225872842258996E07136338
chr154225899842259110E07136608
chr154225913442259394E07136744
chr154225939842259602E07137008
chr154225974242259865E07137352
chr154225988442260391E07137494
chr154226040142260594E07138011
chr154218646242187988E072-34402
chr154219653542197728E072-24662
chr154220524542205538E072-16852
chr154220560742205740E072-16650
chr154220608042206307E072-16083
chr154220635242206964E072-15426
chr154220975142210616E072-11774
chr154221061742211458E072-10932
chr154221371942214354E072-8036
chr154222086642221907E072-483
chr154222194542222112E072-278
chr154222212442222232E072-158
chr154224980742250694E07227417
chr154225784842257934E07235458
chr154225797642258090E07235586
chr154225816642258667E07235776
chr154218613342186413E073-35977
chr154219653542197728E073-24662
chr154220608042206307E073-16083
chr154220635242206964E073-15426
chr154220730442207413E073-14977
chr154220838642208775E073-13615
chr154220880242209263E073-13127
chr154220975142210616E073-11774
chr154221061742211458E073-10932
chr154221281042213310E073-9080
chr154221335942213718E073-8672
chr154221371942214354E073-8036
chr154222086642221907E073-483
chr154222194542222112E073-278
chr154222212442222232E073-158
chr154222227642223283E0730
chr154223777242237850E07315382
chr154223788242237940E07315492
chr154223796642238469E07315576
chr154220496242205103E074-17287
chr154220511442205198E074-17192
chr154220524542205538E074-16852
chr154220560742205740E074-16650
chr154220608042206307E074-16083
chr154220635242206964E074-15426
chr154220770142207844E074-14546
chr154220788942207995E074-14395
chr154220838642208775E074-13615
chr154220880242209263E074-13127
chr154220975142210616E074-11774
chr154221335942213718E074-8672
chr154221371942214354E074-8036
chr154221437142214571E074-7819
chr154222086642221907E074-483
chr154222227642223283E0740
chr154224368442243922E07421294
chr154224415142244205E07421761
chr154224420642244350E07421816
chr154224438742244442E07421997
chr154225939842259602E07437008
chr154225974242259865E07437352
chr154225988442260391E07437494
chr154226040142260594E07438011
chr154218932842189511E081-32879
chr154218963542190057E081-32333
chr154219011842190226E081-32164
chr154222086642221907E081-483








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr154226326142265444E06740871
chr154226326142265444E06840871
chr154226326142265444E06940871
chr154217441842174966E070-47424
chr154226326142265444E07040871
chr154226326142265444E07140871
chr154226326142265444E07240871
chr154226326142265444E07340871
chr154226326142265444E07440871
chr154217441842174966E082-47424
chr154226326142265444E08240871