rs10261069

Homo sapiens
C>T
SEMA3A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0140 (4205/29970,GnomAD)
C==0153 (4458/29118,TOPMED)
C==0097 (486/5008,1000G)
C==0165 (637/3854,ALSPAC)
C==0168 (624/3708,TWINSUK)
chr7:84172336 (GRCh38.p7) (7q21.11)
ND
GWASdb2
1   publication(s)
See rs on genome
48 Enhancers around
24 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.84172336C>T
GRCh37.p13 chr 7NC_000007.13:g.83801652C>T
SEMA3A RefSeqGeneNG_011489.1:g.27566G>A

Gene: SEMA3A, semaphorin 3A(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SEMA3A transcriptNM_006080.2:c.N/AIntron Variant
SEMA3A transcript variant X2XM_005250110.3:c.N/AIntron Variant
SEMA3A transcript variant X5XM_005250111.4:c.N/AIntron Variant
SEMA3A transcript variant X3XM_006715839.3:c.N/AIntron Variant
SEMA3A transcript variant X3XM_011515734.2:c.N/AIntron Variant
SEMA3A transcript variant X6XM_017011673.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.147T=0.853
1000GenomesAmericanSub694C=0.110T=0.890
1000GenomesEast AsianSub1008C=0.011T=0.989
1000GenomesEuropeSub1006C=0.157T=0.843
1000GenomesGlobalStudy-wide5008C=0.097T=0.903
1000GenomesSouth AsianSub978C=0.050T=0.950
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.165T=0.835
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.153T=0.846
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.168T=0.832
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
rs102610690.000386nicotine smoking19268276

eQTL of rs10261069 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 rs10261069 in Fetal Brain

Probe ID Position Gene beta p-value
cg05742308chr7:83824384SEMA3A0.02887109267305067.2879e-9
cg10035469chr7:83824373SEMA3A0.03906529033662718.7421e-9

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 )
chr78377391183774069E067-27583
chr78377410083774220E067-27432
chr78377425183774568E067-27084
chr78381627683817072E06814624
chr78375223683752313E069-49339
chr78375231783752367E069-49285
chr78375479983754864E069-46788
chr78384588983846041E07044237
chr78384618583846445E07044533
chr78375246183752505E071-49147
chr78375258083752675E071-48977
chr78375274183752781E071-48871
chr78375246183752505E072-49147
chr78375258083752675E072-48977
chr78375274183752781E072-48871
chr78377362483773704E072-27948
chr78377391183774069E072-27583
chr78377410083774220E072-27432
chr78377425183774568E072-27084
chr78379082283791014E072-10638
chr78379149483791633E072-10019
chr78379171183791861E072-9791
chr78379196383792317E072-9335
chr78375223683752313E074-49339
chr78375231783752367E074-49285
chr78375246183752505E074-49147
chr78375258083752675E074-48977
chr78375274183752781E074-48871
chr78375313183753919E074-47733
chr78377425183774568E074-27084
chr78377470783774757E074-26895
chr78377520183775465E074-26187
chr78377553283775713E074-25939
chr78379082283791014E074-10638
chr78379149483791633E074-10019
chr78379171183791861E074-9791
chr78379196383792317E074-9335
chr78381382883813925E07412176
chr78381398783814152E07412335
chr78380002883800476E081-1176
chr78380064583800720E081-932
chr78380076983800819E081-833
chr78381939083820002E08117738
chr78382022383820299E08118571
chr78382030983820378E08118657
chr78379957283799642E082-2010
chr78379986783799917E082-1735
chr78381811183818575E08216459









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr78382108883821680E06719436
chr78382210783826051E06720455
chr78382063083821064E06818978
chr78382108883821680E06819436
chr78382168683822049E06820034
chr78382210783826051E06820455
chr78382210783826051E06920455
chr78382108883821680E07019436
chr78382168683822049E07020034
chr78382210783826051E07020455
chr78382210783826051E07120455
chr78382210783826051E07220455
chr78382108883821680E07319436
chr78382168683822049E07320034
chr78382210783826051E07320455
chr78382210783826051E07420455
chr78382063083821064E08118978
chr78382108883821680E08119436
chr78382168683822049E08120034
chr78382210783826051E08120455
chr78382063083821064E08218978
chr78382108883821680E08219436
chr78382168683822049E08220034
chr78382210783826051E08220455