rs2249100

Homo sapiens
C>A
CXADR : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0357 (10691/29928,GnomAD)
C==0401 (11700/29118,TOPMED)
C==0356 (1781/5008,1000G)
C==0337 (1298/3854,ALSPAC)
C==0331 (1228/3708,TWINSUK)
chr21:17557426 (GRCh38.p7) (21q21.1)
ND
GWASdb2
1   publication(s)
See rs on genome
144 Enhancers around
13 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 21NC_000021.9:g.17557426C>A
GRCh37.p13 chr 21NC_000021.8:g.18929744C>A
CXADR RefSeqGeneNG_029458.1:g.49521C>A

Gene: CXADR, coxsackie virus and adenovirus receptor(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CXADR transcript variant 2NM_001207063.1:c.N/AIntron Variant
CXADR transcript variant 3NM_001207064.1:c.N/AIntron Variant
CXADR transcript variant 4NM_001207065.1:c.N/AIntron Variant
CXADR transcript variant 5NM_001207066.1:c.N/AIntron Variant
CXADR transcript variant 1NM_001338.4:c.N/AIntron Variant
CXADR transcript variant X2XM_011529476.2:c.N/AIntron Variant
CXADR transcript variant X3XM_011529477.2:c.N/AIntron Variant
CXADR transcript variant X4XM_011529478.2:c.N/AIntron Variant
CXADR transcript variant X5XM_011529479.1:c.N/AIntron Variant
CXADR transcript variant X1XR_001754814.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.535A=0.465
1000GenomesAmericanSub694C=0.320A=0.680
1000GenomesEast AsianSub1008C=0.233A=0.767
1000GenomesEuropeSub1006C=0.333A=0.667
1000GenomesGlobalStudy-wide5008C=0.356A=0.644
1000GenomesSouth AsianSub978C=0.290A=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.337A=0.663
The Genome Aggregation DatabaseAfricanSub8698C=0.480A=0.520
The Genome Aggregation DatabaseAmericanSub838C=0.290A=0.710
The Genome Aggregation DatabaseEast AsianSub1606C=0.267A=0.733
The Genome Aggregation DatabaseEuropeSub18484C=0.311A=0.688
The Genome Aggregation DatabaseGlobalStudy-wide29928C=0.357A=0.642
The Genome Aggregation DatabaseOtherSub302C=0.290A=0.710
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.401A=0.598
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.331A=0.669
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs22491000.000401nicotine dependence17158188

eQTL of rs2249100 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 rs2249100 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 )
chr211888741218887462E067-42282
chr211888760918887751E067-41993
chr211888781218887852E067-41892
chr211888816418888353E067-41391
chr211888862618888690E067-41054
chr211889513818895876E067-33868
chr211889911018899422E067-30322
chr211889942618900082E067-29662
chr211890014218900376E067-29368
chr211890042618900498E067-29246
chr211890071618900766E067-28978
chr211890113918901251E067-28493
chr211890561618905735E067-24009
chr211890581518905957E067-23787
chr211891402618914210E067-15534
chr211891454918915076E067-14668
chr211891509418915359E067-14385
chr211892669518926846E067-2898
chr211892690618927526E067-2218
chr211893085218931260E0671108
chr211888816418888353E068-41391
chr211888862618888690E068-41054
chr211888884318888893E068-40851
chr211889911018899422E068-30322
chr211889942618900082E068-29662
chr211890014218900376E068-29368
chr211890476818904845E068-24899
chr211890966818909953E068-19791
chr211890996718910080E068-19664
chr211891175818911884E068-17860
chr211891221318912410E068-17334
chr211891454918915076E068-14668
chr211891509418915359E068-14385
chr211892060918921049E068-8695
chr211892108218921168E068-8576
chr211892669518926846E068-2898
chr211892690618927526E068-2218
chr211893307518933141E0683331
chr211889495118895070E069-34674
chr211889513818895876E069-33868
chr211889911018899422E069-30322
chr211889942618900082E069-29662
chr211890444018904490E069-25254
chr211890476818904845E069-24899
chr211890561618905735E069-24009
chr211890581518905957E069-23787
chr211890868618909126E069-20618
chr211890966818909953E069-19791
chr211890996718910080E069-19664
chr211891454918915076E069-14668
chr211891509418915359E069-14385
chr211892669518926846E069-2898
chr211892690618927526E069-2218
chr211893085218931260E0691108
chr211893279318932941E0693049
chr211893307518933141E0693331
chr211888741218887462E070-42282
chr211891454918915076E070-14668
chr211891509418915359E070-14385
chr211889911018899422E071-30322
chr211889942618900082E071-29662
chr211890014218900376E071-29368
chr211890561618905735E071-24009
chr211890581518905957E071-23787
chr211890861918908673E071-21071
chr211890868618909126E071-20618
chr211890966818909953E071-19791
chr211890996718910080E071-19664
chr211891107618911126E071-18618
chr211891454918915076E071-14668
chr211891509418915359E071-14385
chr211891544018915516E071-14228
chr211891558118915635E071-14109
chr211892060918921049E071-8695
chr211892108218921168E071-8576
chr211892646318926517E071-3227
chr211892793618927986E071-1758
chr211892834518928472E071-1272
chr211892855918928609E071-1135
chr211888741218887462E072-42282
chr211888760918887751E072-41993
chr211888781218887852E072-41892
chr211888816418888353E072-41391
chr211889495118895070E072-34674
chr211889851618898570E072-31174
chr211889911018899422E072-30322
chr211889942618900082E072-29662
chr211890014218900376E072-29368
chr211891454918915076E072-14668
chr211891509418915359E072-14385
chr211891544018915516E072-14228
chr211891558118915635E072-14109
chr211891963618919690E072-10054
chr211892646318926517E072-3227
chr211892669518926846E072-2898
chr211892690618927526E072-2218
chr211893085218931260E0721108
chr211888741218887462E073-42282
chr211888760918887751E073-41993
chr211888781218887852E073-41892
chr211888816418888353E073-41391
chr211888862618888690E073-41054
chr211888884318888893E073-40851
chr211891454918915076E073-14668
chr211891509418915359E073-14385
chr211892669518926846E073-2898
chr211892690618927526E073-2218
chr211888741218887462E074-42282
chr211888760918887751E074-41993
chr211888781218887852E074-41892
chr211888816418888353E074-41391
chr211888862618888690E074-41054
chr211888884318888893E074-40851
chr211888897018889041E074-40703
chr211889942618900082E074-29662
chr211890476818904845E074-24899
chr211890561618905735E074-24009
chr211890581518905957E074-23787
chr211890966818909953E074-19791
chr211891509418915359E074-14385
chr211892646318926517E074-3227
chr211892669518926846E074-2898
chr211892690618927526E074-2218
chr211892834518928472E074-1272
chr211892855918928609E074-1135
chr211893085218931260E0741108
chr211893279318932941E0743049
chr211893307518933141E0743331
chr211888741218887462E081-42282
chr211888760918887751E081-41993
chr211889911018899422E081-30322
chr211889942618900082E081-29662
chr211891376218913802E081-15942
chr211891402618914210E081-15534
chr211891454918915076E081-14668
chr211891509418915359E081-14385
chr211891544018915516E081-14228
chr211891558118915635E081-14109
chr211888741218887462E082-42282
chr211888760918887751E082-41993
chr211891454918915076E082-14668
chr211891509418915359E082-14385
chr211891544018915516E082-14228
chr211891558118915635E082-14109










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr211888391418886935E067-42809
chr211888391418886935E068-42809
chr211888391418886935E069-42809
chr211888391418886935E070-42809
chr211888700118887131E070-42613
chr211888391418886935E071-42809
chr211888391418886935E072-42809
chr211888391418886935E073-42809
chr211888391418886935E074-42809
chr211888391418886935E081-42809
chr211888391418886935E082-42809
chr211888700118887131E082-42613
chr211888717918887249E082-42495