rs2297301

Homo sapiens
T>C
SYNE2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0030 (3653/121138,ExAC)
C=0024 (739/29984,GnomAD)
C=0015 (441/29118,TOPMED)
T==0015 (197/13006,GO-ESP)
C=0039 (193/5008,1000G)
C=0019 (73/3854,ALSPAC)
C=0023 (86/3708,TWINSUK)
chr14:64177487 (GRCh38.p7) (14q23.2)
ND
GWASdb2
1   publication(s)
See rs on genome
51 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 14NC_000014.9:g.64177487T>C
GRCh37.p13 chr 14NC_000014.8:g.64644205T>C
SYNE2 RefSeqGeneNG_011756.1:g.329523T>C

Gene: SYNE2, spectrin repeat containing nuclear envelope protein 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SYNE2 transcript variant 1NM_015180.4:c.N/AIntron Variant
SYNE2 transcript variant 5NM_182914.2:c.N/AIntron Variant
SYNE2 transcript variant 2NM_182910.2:c.N/AGenic Upstream Transcript Variant
SYNE2 transcript variant 4NM_182913.2:c.N/AGenic Upstream Transcript Variant
SYNE2 transcript variant X7XM_005267454.1:c.N/AIntron Variant
SYNE2 transcript variant X9XM_005267456.1:c.N/AIntron Variant
SYNE2 transcript variant X13XM_005267457.1:c.N/AIntron Variant
SYNE2 transcript variant X14XM_005267458.1:c.N/AIntron Variant
SYNE2 transcript variant X16XM_005267459.1:c.N/AIntron Variant
SYNE2 transcript variant X1XM_011536574.1:c.N/AIntron Variant
SYNE2 transcript variant X2XM_011536575.2:c.N/AIntron Variant
SYNE2 transcript variant X4XM_011536576.2:c.N/AIntron Variant
SYNE2 transcript variant X3XM_011536577.2:c.N/AIntron Variant
SYNE2 transcript variant X6XM_011536578.1:c.N/AIntron Variant
SYNE2 transcript variant X8XM_011536579.1:c.N/AIntron Variant
SYNE2 transcript variant X10XM_011536580.1:c.N/AIntron Variant
SYNE2 transcript variant X12XM_011536581.1:c.N/AIntron Variant
SYNE2 transcript variant X15XM_011536582.1:c.N/AIntron Variant
SYNE2 transcript variant X5XM_017021101.1:c.N/AIntron Variant
SYNE2 transcript variant X11XM_017021102.1:c.N/AIntron Variant
SYNE2 transcript variant X19XM_017021103.1:c.N/AGenic Upstream Transcript Variant
SYNE2 transcript variant X20XM_017021104.1:c.N/AGenic Upstream Transcript Variant
SYNE2 transcript variant X18XM_011536584.2:c.N/AGenic Downstream Transcript Variant
SYNE2 transcript variant X17XR_001750198.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.998C=0.002
1000GenomesAmericanSub694T=0.970C=0.030
1000GenomesEast AsianSub1008T=0.891C=0.109
1000GenomesEuropeSub1006T=0.977C=0.023
1000GenomesGlobalStudy-wide5008T=0.961C=0.039
1000GenomesSouth AsianSub978T=0.960C=0.040
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.981C=0.019
The Exome Aggregation ConsortiumAmericanSub21832T=0.994C=0.006
The Exome Aggregation ConsortiumAsianSub25142T=0.935C=0.064
The Exome Aggregation ConsortiumEuropeSub73258T=0.974C=0.025
The Exome Aggregation ConsortiumGlobalStudy-wide121138T=0.969C=0.030
The Exome Aggregation ConsortiumOtherSub906T=0.980C=0.020
The Genome Aggregation DatabaseAfricanSub8724T=0.996C=0.004
The Genome Aggregation DatabaseAmericanSub838T=1.000C=0.000
The Genome Aggregation DatabaseEast AsianSub1620T=0.878C=0.122
The Genome Aggregation DatabaseEuropeSub18500T=0.973C=0.026
The Genome Aggregation DatabaseGlobalStudy-wide29984T=0.975C=0.024
The Genome Aggregation DatabaseOtherSub302T=0.990C=0.010
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.984C=0.015
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.977C=0.023
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
rs22973010.000986nicotine smoking19268276

eQTL of rs2297301 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 rs2297301 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 )
chr146466270164662925E06718496
chr146466306264663135E06718857
chr146466560564665695E06721400
chr146466570064665952E06721495
chr146466601764666080E06721812
chr146468802764688782E06743822
chr146466185864662656E06817653
chr146466270164662925E06818496
chr146466306264663135E06818857
chr146468779064687943E06843585
chr146466270164662925E06918496
chr146466306264663135E06918857
chr146466487764665103E06920672
chr146466510664665592E06920901
chr146466560564665695E06921400
chr146466570064665952E06921495
chr146468779064687943E06943585
chr146466270164662925E07018496
chr146466306264663135E07018857
chr146466185864662656E07117653
chr146466270164662925E07118496
chr146466306264663135E07118857
chr146466469364664743E07120488
chr146466487764665103E07120672
chr146466510664665592E07120901
chr146466560564665695E07121400
chr146466570064665952E07121495
chr146466601764666080E07121812
chr146468779064687943E07143585
chr146466270164662925E07218496
chr146466306264663135E07218857
chr146466694464667473E07222739
chr146466510664665592E07320901
chr146466560564665695E07321400
chr146466570064665952E07321495
chr146466601764666080E07321812
chr146466510664665592E07420901
chr146466694464667473E07422739
chr146466748764668068E07423282
chr146466270164662925E08118496
chr146466306264663135E08118857
chr146466469364664743E08120488
chr146466487764665103E08120672
chr146466510664665592E08120901
chr146466748764668068E08123282
chr146466807564668369E08123870
chr146466849864668892E08124293
chr146466908964669176E08124884
chr146468382064683925E08139615
chr146468398164684441E08139776
chr146467165764671751E08227452










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr146466321964664280E06719014
chr146466445364664517E06720248
chr146466457364664681E06720368
chr146466321964664280E06819014
chr146466445364664517E06820248
chr146466457364664681E06820368
chr146466321964664280E06919014
chr146466445364664517E06920248
chr146466457364664681E06920368
chr146466321964664280E07019014
chr146466445364664517E07020248
chr146466457364664681E07020368
chr146466321964664280E07119014
chr146466445364664517E07120248
chr146466457364664681E07120368
chr146466321964664280E07219014
chr146466445364664517E07220248
chr146466457364664681E07220368
chr146466321964664280E07319014
chr146466445364664517E07320248
chr146466457364664681E07320368
chr146466321964664280E07419014
chr146466445364664517E07420248
chr146466457364664681E07420368
chr146466321964664280E08119014
chr146466445364664517E08120248
chr146466321964664280E08219014
chr146466445364664517E08220248
chr146466457364664681E08220368