rs12623730

Homo sapiens
C>T
TSSC1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0279 (8384/29956,GnomAD)
T=0323 (9407/29116,TOPMED)
T=0407 (2037/5008,1000G)
T=0141 (543/3854,ALSPAC)
T=0144 (535/3708,TWINSUK)
chr2:3330232 (GRCh38.p7) (2p25.3)
ND
GWASdb2
1   publication(s)
See rs on genome
166 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.3330232C>T
GRCh37.p13 chr 2NC_000002.11:g.3334003C>T

Gene: TSSC1, tumor suppressing subtransferable candidate 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TSSC1 transcriptNM_003310.2:c.N/AIntron Variant
TSSC1 transcript variant X1XM_011510383.2:c.N/AIntron Variant
TSSC1 transcript variant X2XM_011510384.2:c.N/AIntron Variant
EIPR1 transcript variant X2XM_011510385.2:c.N/AIntron Variant
TSSC1 transcript variant X6XM_011510387.2:c.N/AIntron Variant
TSSC1 transcript variant X4XM_017004818.1:c.N/AIntron Variant
EIPR1 transcript variant X4XM_006711893.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.472T=0.528
1000GenomesAmericanSub694C=0.830T=0.170
1000GenomesEast AsianSub1008C=0.376T=0.624
1000GenomesEuropeSub1006C=0.816T=0.184
1000GenomesGlobalStudy-wide5008C=0.593T=0.407
1000GenomesSouth AsianSub978C=0.590T=0.410
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.859T=0.141
The Genome Aggregation DatabaseAfricanSub8716C=0.510T=0.490
The Genome Aggregation DatabaseAmericanSub838C=0.810T=0.190
The Genome Aggregation DatabaseEast AsianSub1614C=0.343T=0.657
The Genome Aggregation DatabaseEuropeSub18486C=0.846T=0.154
The Genome Aggregation DatabaseGlobalStudy-wide29956C=0.720T=0.279
The Genome Aggregation DatabaseOtherSub302C=0.840T=0.160
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.676T=0.323
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.856T=0.144
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs126237308.59E-05nicotine dependence (smoking)22377092

eQTL of rs12623730 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 rs12623730 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 )
chr232869423287003E067-47000
chr232870203287101E067-46902
chr232871613287392E067-46611
chr232874373287487E067-46516
chr232884743288570E067-45433
chr232923013292597E067-41406
chr232927093293177E067-40826
chr232934323293577E067-40426
chr233067863307043E067-26960
chr233611913361241E06727188
chr233613583361485E06727355
chr232870203287101E068-46902
chr232871613287392E068-46611
chr232900363290099E068-43904
chr232904773290528E068-43475
chr232905643290654E068-43349
chr232934323293577E068-40426
chr233605923360910E06826589
chr233611913361241E06827188
chr233613583361485E06827355
chr232869423287003E069-47000
chr232870203287101E069-46902
chr232871613287392E069-46611
chr232874373287487E069-46516
chr232900363290099E069-43904
chr232904773290528E069-43475
chr232905643290654E069-43349
chr232923013292597E069-41406
chr232927093293177E069-40826
chr232934323293577E069-40426
chr232945383294708E069-39295
chr233067863307043E069-26960
chr233078653307928E069-26075
chr233079563307996E069-26007
chr233529113353502E06918908
chr232847943284848E070-49155
chr232850983285176E070-48827
chr232869423287003E070-47000
chr232870203287101E070-46902
chr232871613287392E070-46611
chr232890663289113E070-44890
chr232891573289269E070-44734
chr232893133289363E070-44640
chr232900363290099E070-43904
chr232904773290528E070-43475
chr232905643290654E070-43349
chr232923013292597E070-41406
chr232934323293577E070-40426
chr233062353306291E070-27712
chr233064443306780E070-27223
chr233078653307928E070-26075
chr233079563307996E070-26007
chr232869423287003E071-47000
chr232870203287101E071-46902
chr232871613287392E071-46611
chr232884743288570E071-45433
chr232890663289113E071-44890
chr232891573289269E071-44734
chr232893133289363E071-44640
chr232900363290099E071-43904
chr232904773290528E071-43475
chr232905643290654E071-43349
chr232927093293177E071-40826
chr232934323293577E071-40426
chr232945383294708E071-39295
chr233067863307043E071-26960
chr232869423287003E072-47000
chr232870203287101E072-46902
chr232871613287392E072-46611
chr232900363290099E072-43904
chr232904773290528E072-43475
chr232905643290654E072-43349
chr232923013292597E072-41406
chr232927093293177E072-40826
chr233067863307043E072-26960
chr233078653307928E072-26075
chr233079563307996E072-26007
chr233669393367020E07232936
chr232923013292597E073-41406
chr232927093293177E073-40826
chr232934323293577E073-40426
chr232945383294708E073-39295
chr232968573297009E073-36994
chr232970973297193E073-36810
chr232973373297412E073-36591
chr233071713307838E073-26165
chr233078653307928E073-26075
chr233079563307996E073-26007
chr233529113353502E07318908
chr232857003286771E074-47232
chr232869423287003E074-47000
chr232870203287101E074-46902
chr232871613287392E074-46611
chr232904773290528E074-43475
chr232905643290654E074-43349
chr232923013292597E074-41406
chr232927093293177E074-40826
chr232934323293577E074-40426
chr233067863307043E074-26960
chr233071713307838E074-26165
chr233611913361241E07427188
chr233613583361485E07427355
chr232847943284848E081-49155
chr232850983285176E081-48827
chr232857003286771E081-47232
chr232869423287003E081-47000
chr232870203287101E081-46902
chr232871613287392E081-46611
chr232874373287487E081-46516
chr232884743288570E081-45433
chr232890663289113E081-44890
chr232891573289269E081-44734
chr232893133289363E081-44640
chr232900363290099E081-43904
chr232904773290528E081-43475
chr232905643290654E081-43349
chr232923013292597E081-41406
chr232927093293177E081-40826
chr232934323293577E081-40426
chr232945383294708E081-39295
chr232956373295687E081-38316
chr232963363296569E081-37434
chr232966183296786E081-37217
chr232968573297009E081-36994
chr232970973297193E081-36810
chr232973373297412E081-36591
chr232975743297640E081-36363
chr232979283298037E081-35966
chr233034093303576E081-30427
chr233036893303789E081-30214
chr233042583304373E081-29630
chr233045223304626E081-29377
chr233062353306291E081-27712
chr233064443306780E081-27223
chr233067863307043E081-26960
chr233071713307838E081-26165
chr233078653307928E081-26075
chr233079563307996E081-26007
chr233174443317617E081-16386
chr233177973318106E081-15897
chr233184643318618E081-15385
chr233381113339171E0814108
chr233529113353502E08118908
chr233794033379495E08145400
chr233795933379685E08145590
chr233797493379789E08145746
chr233801033380174E08146100
chr232847943284848E082-49155
chr232850983285176E082-48827
chr232869423287003E082-47000
chr232870203287101E082-46902
chr232871613287392E082-46611
chr232874373287487E082-46516
chr232884743288570E082-45433
chr232890663289113E082-44890
chr232891573289269E082-44734
chr232893133289363E082-44640
chr232900363290099E082-43904
chr232923013292597E082-41406
chr232934323293577E082-40426
chr232945383294708E082-39295
chr232963363296569E082-37434
chr233062353306291E082-27712
chr233064443306780E082-27223
chr233067863307043E082-26960
chr233081103308169E082-25834










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr233810833382440E06747080
chr233810833382440E06847080
chr233810833382440E06947080
chr233810833382440E07047080
chr233810833382440E07147080
chr233810833382440E07247080
chr233810833382440E07347080
chr233810833382440E07447080
chr233810833382440E08147080
chr233810833382440E08247080