rs2247219

Homo sapiens
T>G
SEMA3E : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0275 (8216/29868,GnomAD)
T==0310 (9053/29118,TOPMED)
T==0237 (1187/5008,1000G)
T==0237 (914/3854,ALSPAC)
T==0235 (870/3708,TWINSUK)
chr7:83438154 (GRCh38.p7) (7q21.11)
ND
GWASdb2
2   publication(s)
See rs on genome
37 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.83438154T>G
GRCh37.p13 chr 7NC_000007.13:g.83067470T>G
SEMA3E RefSeqGeneNG_021242.1:g.216010A>C

Gene: SEMA3E, semaphorin 3E(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SEMA3E transcript variant 2NM_001178129.1:c.N/AIntron Variant
SEMA3E transcript variant 1NM_012431.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.507G=0.493
1000GenomesAmericanSub694T=0.160G=0.840
1000GenomesEast AsianSub1008T=0.004G=0.996
1000GenomesEuropeSub1006T=0.234G=0.766
1000GenomesGlobalStudy-wide5008T=0.237G=0.763
1000GenomesSouth AsianSub978T=0.170G=0.830
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.237G=0.763
The Genome Aggregation DatabaseAfricanSub8712T=0.438G=0.562
The Genome Aggregation DatabaseAmericanSub828T=0.180G=0.820
The Genome Aggregation DatabaseEast AsianSub1618T=0.001G=0.999
The Genome Aggregation DatabaseEuropeSub18408T=0.226G=0.773
The Genome Aggregation DatabaseGlobalStudy-wide29868T=0.275G=0.724
The Genome Aggregation DatabaseOtherSub302T=0.270G=0.730
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.310G=0.689
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.235G=0.765
PMID Title Author Journal
22536871Convergence of genetic influences in comorbidity.McEachin RCBMC Bioinformatics
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs22472196.23E-06alcohol and nictotine co-dependence20158304

eQTL of rs2247219 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 rs2247219 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 )
chr78308086083081326E06713390
chr78309741083098115E06729940
chr78308086083081326E06813390
chr78309741083098115E06829940
chr78306813683068717E069666
chr78309741083098115E06929940
chr78307550083075739E0708030
chr78307574283075876E0708272
chr78307591083075961E0708440
chr78308086083081326E07013390
chr78308143783081517E07013967
chr78308152383081699E07014053
chr78308172583081839E07014255
chr78310594483106126E07038474
chr78306813683068717E071666
chr78308086083081326E07113390
chr78306813683068717E072666
chr78308086083081326E07213390
chr78309741083098115E07229940
chr78309830183098839E07230831
chr78309885383099021E07231383
chr78306813683068717E073666
chr78306813683068717E074666
chr78306929683069346E0741826
chr78308086083081326E07413390
chr78308143783081517E07413967
chr78308152383081699E07414053
chr78308172583081839E07414255
chr78309741083098115E07429940
chr78303839583038520E081-28950
chr78308143783081517E08113967
chr78308152383081699E08114053
chr78311639483116650E08148924
chr78308086083081326E08213390
chr78308143783081517E08213967
chr78308152383081699E08214053
chr78308172583081839E08214255