rs1858030

Homo sapiens
G>A
SDK2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0316 (9471/29928,GnomAD)
A=0320 (9317/29118,TOPMED)
A=0292 (1462/5008,1000G)
A=0347 (1336/3854,ALSPAC)
A=0358 (1327/3708,TWINSUK)
chr17:73626530 (GRCh38.p7) (17q25.1)
ND
GWASdb2
1   publication(s)
See rs on genome
150 Enhancers around
17 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.73626530G>A
GRCh37.p13 chr 17NC_000017.10:g.71622669G>A

Gene: SDK2, sidekick cell adhesion molecule 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SDK2 transcriptNM_001144952.1:c.N/AIntron Variant
SDK2 transcript variant X1XM_011524914.2:c.N/AIntron Variant
SDK2 transcript variant X2XM_011524915.2:c.N/AIntron Variant
SDK2 transcript variant X3XM_011524916.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.678A=0.322
1000GenomesAmericanSub694G=0.720A=0.280
1000GenomesEast AsianSub1008G=0.814A=0.186
1000GenomesEuropeSub1006G=0.679A=0.321
1000GenomesGlobalStudy-wide5008G=0.708A=0.292
1000GenomesSouth AsianSub978G=0.660A=0.340
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.653A=0.347
The Genome Aggregation DatabaseAfricanSub8718G=0.687A=0.313
The Genome Aggregation DatabaseAmericanSub838G=0.710A=0.290
The Genome Aggregation DatabaseEast AsianSub1616G=0.845A=0.155
The Genome Aggregation DatabaseEuropeSub18454G=0.667A=0.332
The Genome Aggregation DatabaseGlobalStudy-wide29928G=0.683A=0.316
The Genome Aggregation DatabaseOtherSub302G=0.640A=0.360
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.680A=0.320
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.642A=0.358
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
rs18580300.000896nicotine dependence17158188

eQTL of rs1858030 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 rs1858030 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 )
chr177162644271626501E0673773
chr177162670571626970E0674036
chr177162708571627159E0674416
chr177162733571627475E0674666
chr177162753971627589E0674870
chr177163648671636573E06713817
chr177161217371612231E068-10438
chr177161223271612365E068-10304
chr177161238971612441E068-10228
chr177162199971622954E0680
chr177162708571627159E0684416
chr177162733571627475E0684666
chr177162753971627589E0684870
chr177158331371583940E069-38729
chr177162199971622954E0690
chr177162612671626284E0693457
chr177162644271626501E0693773
chr177162670571626970E0694036
chr177162708571627159E0694416
chr177162733571627475E0694666
chr177162753971627589E0694870
chr177163606871636350E06913399
chr177163648671636573E06913817
chr177163800071638495E06915331
chr177157276471572814E070-49855
chr177157318071573247E070-49422
chr177157337771573475E070-49194
chr177157544471575494E070-47175
chr177157557471575624E070-47045
chr177157630271576518E070-46151
chr177157664271576705E070-45964
chr177157678071576834E070-45835
chr177157707971577133E070-45536
chr177157757671577616E070-45053
chr177157771671577756E070-44913
chr177157819571578251E070-44418
chr177157855671578776E070-43893
chr177157901571579149E070-43520
chr177157940971579449E070-43220
chr177158001671580056E070-42613
chr177159585171597091E070-25578
chr177160814871608197E070-14472
chr177160823971608561E070-14108
chr177160913971610726E070-11943
chr177161223271612365E070-10304
chr177161956271619616E070-3053
chr177161967671619750E070-2919
chr177163533771635440E07012668
chr177163550671636060E07012837
chr177163606871636350E07013399
chr177163648671636573E07013817
chr177163672371636773E07014054
chr177163758071637672E07014911
chr177163779971637898E07015130
chr177164205571642179E07019386
chr177164225771642530E07019588
chr177164255371642788E07019884
chr177164280371643317E07020134
chr177164336671643759E07020697
chr177164393671643988E07021267
chr177162670571626970E0714036
chr177162708571627159E0714416
chr177162733571627475E0714666
chr177162753971627589E0714870
chr177163779971637898E07115130
chr177166310171663176E07140432
chr177166336171663702E07140692
chr177166376671663903E07141097
chr177161203271612149E072-10520
chr177162670571626970E0724036
chr177162708571627159E0724416
chr177162733571627475E0724666
chr177162753971627589E0724870
chr177163550671636060E07212837
chr177163606871636350E07213399
chr177163800071638495E07215331
chr177164205571642179E07219386
chr177164225771642530E07219588
chr177164255371642788E07219884
chr177162670571626970E0734036
chr177162708571627159E0734416
chr177162733571627475E0734666
chr177162670571626970E0744036
chr177162708571627159E0744416
chr177162733571627475E0744666
chr177162753971627589E0744870
chr177163606871636350E07413399
chr177157544471575494E081-47175
chr177157557471575624E081-47045
chr177157630271576518E081-46151
chr177157664271576705E081-45964
chr177157678071576834E081-45835
chr177157707971577133E081-45536
chr177157757671577616E081-45053
chr177157771671577756E081-44913
chr177157819571578251E081-44418
chr177157855671578776E081-43893
chr177158245871582626E081-40043
chr177158264671582742E081-39927
chr177159049971590618E081-32051
chr177159074971590882E081-31787
chr177159088571590948E081-31721
chr177159097971591064E081-31605
chr177159110971591256E081-31413
chr177160002471600074E081-22595
chr177160012671600210E081-22459
chr177160913971610726E081-11943
chr177161177271611912E081-10757
chr177161217371612231E081-10438
chr177161223271612365E081-10304
chr177161238971612441E081-10228
chr177161248371613454E081-9215
chr177161355471613733E081-8936
chr177161388371613933E081-8736
chr177161408871614132E081-8537
chr177161414071614206E081-8463
chr177163533771635440E08112668
chr177163550671636060E08112837
chr177163606871636350E08113399
chr177163648671636573E08113817
chr177163672371636773E08114054
chr177163758071637672E08114911
chr177163779971637898E08115130
chr177163800071638495E08115331
chr177164205571642179E08119386
chr177164225771642530E08119588
chr177164255371642788E08119884
chr177164280371643317E08120134
chr177164336671643759E08120697
chr177164393671643988E08121267
chr177164423571644491E08121566
chr177164455671644606E08121887
chr177164712371647217E08124454
chr177164728271647334E08124613
chr177164735271647402E08124683
chr177157630271576518E082-46151
chr177157664271576705E082-45964
chr177157678071576834E082-45835
chr177160823971608561E082-14108
chr177160880771608932E082-13737
chr177161217371612231E082-10438
chr177161223271612365E082-10304
chr177161238971612441E082-10228
chr177161248371613454E082-9215
chr177161408871614132E082-8537
chr177164225771642530E08219588
chr177164255371642788E08219884
chr177164280371643317E08220134
chr177164336671643759E08220697
chr177164393671643988E08221267










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr177163893271640117E06716263
chr177164015771642052E06717488
chr177163893271640117E06816263
chr177164015771642052E06817488
chr177163893271640117E06916263
chr177164015771642052E06917488
chr177164015771642052E07017488
chr177164015771642052E07117488
chr177163893271640117E07216263
chr177164015771642052E07217488
chr177163883171638871E07316162
chr177163893271640117E07316263
chr177164015771642052E07317488
chr177163893271640117E07416263
chr177164015771642052E07417488
chr177163893271640117E08216263
chr177164015771642052E08217488