rs2836823

Homo sapiens
C>T
LOC102724740 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0304 (9122/29922,GnomAD)
T=0264 (7702/29118,TOPMED)
T=0199 (995/5008,1000G)
T=0476 (1836/3854,ALSPAC)
T=0484 (1794/3708,TWINSUK)
chr21:39008323 (GRCh38.p7) (21q22.2)
ND
GWASdb2 | GWASCatalog
4   publication(s)
See rs on genome
86 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 21NC_000021.9:g.39008323C>T
GRCh37.p13 chr 21NC_000021.8:g.40380249C>T

Gene: LOC102724740, uncharacterized LOC102724740(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC102724740 transcript variant X2XR_001755043.1:n.N/AIntron Variant
LOC102724740 transcript variant X6XR_001755044.1:n.N/AIntron Variant
LOC102724740 transcript variant X7XR_001755045.1:n.N/AIntron Variant
LOC102724740 transcript variant X8XR_001755046.1:n.N/AIntron Variant
LOC102724740 transcript variant X9XR_001755047.1:n.N/AIntron Variant
LOC102724740 transcript variant X10XR_001755048.1:n.N/AIntron Variant
LOC102724740 transcript variant X11XR_001755049.1:n.N/AIntron Variant
LOC102724740 transcript variant X1XR_430375.3:n.N/AIntron Variant
LOC102724740 transcript variant X3XR_937714.2:n.N/AIntron Variant
LOC102724740 transcript variant X4XR_937715.2:n.N/AIntron Variant
LOC102724740 transcript variant X5XR_937716.2:n.N/AIntron Variant
LOC102724740 transcript variant X12XR_001755050.1:n.N/AGenic Upstream Transcript Variant
LOC102724740 transcript variant X13XR_001755052.1:n.N/AGenic Upstream Transcript Variant
LOC102724740 transcript variant X14XR_001755053.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.977T=0.023
1000GenomesAmericanSub694C=0.600T=0.400
1000GenomesEast AsianSub1008C=0.963T=0.037
1000GenomesEuropeSub1006C=0.528T=0.472
1000GenomesGlobalStudy-wide5008C=0.801T=0.199
1000GenomesSouth AsianSub978C=0.820T=0.180
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.524T=0.476
The Genome Aggregation DatabaseAfricanSub8716C=0.915T=0.085
The Genome Aggregation DatabaseAmericanSub828C=0.670T=0.330
The Genome Aggregation DatabaseEast AsianSub1622C=0.961T=0.039
The Genome Aggregation DatabaseEuropeSub18454C=0.569T=0.430
The Genome Aggregation DatabaseGlobalStudy-wide29922C=0.695T=0.304
The Genome Aggregation DatabaseOtherSub302C=0.680T=0.320
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.735T=0.264
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.516T=0.484
PMID Title Author Journal
18565990Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence.Saccone SFBioinformatics
19184766A testable prognostic model of nicotine dependence.Ramoni RBJ Neurogenet
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet
21618602Detecting genetic interactions for quantitative traits with U-statistics.Li MGenet Epidemiol

P-Value

SNP ID p-value Traits Study
rs28368232E-06nicotine dependence17158188

eQTL of rs2836823 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 rs2836823 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 )
chr214033030340330561E067-49688
chr214033646140336579E067-43670
chr214033659740336737E067-43512
chr214036143840362696E067-17553
chr214036849240368542E068-11707
chr214036891740368957E068-11292
chr214036904740369190E068-11059
chr214037575740377631E068-2618
chr214037765140377804E068-2445
chr214037806740378148E068-2101
chr214037821840378289E068-1960
chr214037835740379253E068-996
chr214037936440379499E068-750
chr214037953640379694E068-555
chr214037976240379978E068-271
chr214041209240412209E06831843
chr214041250540412797E06832256
chr214035640340358247E069-22002
chr214036428840364436E069-15813
chr214037575740377631E069-2618
chr214037765140377804E069-2445
chr214042873440428842E06948485
chr214042904040429111E06948791
chr214042924640429559E06948997
chr214035836140358438E070-21811
chr214035851640358560E070-21689
chr214035859540358645E070-21604
chr214035876540359030E070-21219
chr214035913440361287E070-18962
chr214036132740361413E070-18836
chr214036271540362941E070-17308
chr214042829540428702E07048046
chr214042873440428842E07048485
chr214042904040429111E07048791
chr214035876540359030E071-21219
chr214035913440361287E071-18962
chr214036132740361413E071-18836
chr214036143840362696E071-17553
chr214036428840364436E071-15813
chr214036447140366436E071-13813
chr214037215840372242E071-8007
chr214037235540372902E071-7347
chr214037575740377631E071-2618
chr214037765140377804E071-2445
chr214037806740378148E071-2101
chr214037821840378289E071-1960
chr214037835740379253E071-996
chr214038055640380652E071307
chr214038070240380742E071453
chr214042873440428842E07148485
chr214042904040429111E07148791
chr214042924640429559E07148997
chr214033030340330561E072-49688
chr214033066240331973E072-48276
chr214036132740361413E072-18836
chr214036143840362696E072-17553
chr214037575740377631E072-2618
chr214037835740379253E072-996
chr214033030340330561E073-49688
chr214036132740361413E073-18836
chr214036143840362696E073-17553
chr214036670240366780E073-13469
chr214036679040366932E073-13317
chr214036725940368135E073-12114
chr214037575740377631E073-2618
chr214037765140377804E073-2445
chr214042698140427040E07346732
chr214042716840427655E07346919
chr214035640340358247E074-22002
chr214035876540359030E074-21219
chr214035913440361287E074-18962
chr214036143840362696E074-17553
chr214036271540362941E074-17308
chr214036318740363340E074-16909
chr214037575740377631E074-2618
chr214037765140377804E074-2445
chr214037806740378148E074-2101
chr214037821840378289E074-1960
chr214038070240380742E074453
chr214042829540428702E07448046
chr214042873440428842E07448485
chr214042904040429111E07448791
chr214036143840362696E081-17553
chr214036271540362941E081-17308
chr214035876540359030E082-21219
chr214036143840362696E082-17553