rs17477949

Homo sapiens
C>T
MICAL2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0279 (8370/29926,GnomAD)
T=0248 (7231/29118,TOPMED)
T=0202 (1012/5008,1000G)
T=0431 (1662/3854,ALSPAC)
T=0421 (1562/3708,TWINSUK)
chr11:12197656 (GRCh38.p7) (11p15.3)
ND
GWASdb2
2   publication(s)
See rs on genome
291 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.12197656C>T
GRCh37.p13 chr 11NC_000011.9:g.12219203C>T

Gene: MICAL2, microtubule associated monooxygenase, calponin and LIM domain containing 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MICAL2 transcript variant 2NM_001282663.1:c.N/AIntron Variant
MICAL2 transcript variant 3NM_001282664.1:c.N/AIntron Variant
MICAL2 transcript variant 4NM_001282665.1:c.N/AIntron Variant
MICAL2 transcript variant 5NM_001282666.1:c.N/AIntron Variant
MICAL2 transcript variant 6NM_001282667.1:c.N/AIntron Variant
MICAL2 transcript variant 7NM_001282668.1:c.N/AIntron Variant
MICAL2 transcript variant 1NM_014632.3:c.N/AIntron Variant
MICAL2 transcript variant X1XM_011520490.2:c.N/AIntron Variant
MICAL2 transcript variant X3XM_011520491.2:c.N/AIntron Variant
MICAL2 transcript variant X4XM_017018589.1:c.N/AIntron Variant
MICAL2 transcript variant X5XM_017018590.1:c.N/AIntron Variant
MICAL2 transcript variant X6XM_017018591.1:c.N/AIntron Variant
MICAL2 transcript variant X2XR_001748049.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.965T=0.035
1000GenomesAmericanSub694C=0.720T=0.280
1000GenomesEast AsianSub1008C=0.947T=0.053
1000GenomesEuropeSub1006C=0.610T=0.390
1000GenomesGlobalStudy-wide5008C=0.798T=0.202
1000GenomesSouth AsianSub978C=0.660T=0.340
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.569T=0.431
The Genome Aggregation DatabaseAfricanSub8716C=0.907T=0.093
The Genome Aggregation DatabaseAmericanSub836C=0.670T=0.330
The Genome Aggregation DatabaseEast AsianSub1622C=0.953T=0.047
The Genome Aggregation DatabaseEuropeSub18450C=0.617T=0.383
The Genome Aggregation DatabaseGlobalStudy-wide29926C=0.720T=0.279
The Genome Aggregation DatabaseOtherSub302C=0.530T=0.470
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.751T=0.248
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.579T=0.421
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet
22719919Glutamate and synaptic plasticity systems and smoking behavior: results from a genetic association study.dos Santos VAPLoS One

P-Value

SNP ID p-value Traits Study
rs174779493.73E-05nicotine smoking19268276

eQTL of rs17477949 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 rs17477949 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 )
chr111217756612177616E067-41587
chr111217787412177933E067-41270
chr111217803712178077E067-41126
chr111217811912178519E067-40684
chr111217852812178679E067-40524
chr111217995612180006E067-39197
chr111218020012180405E067-38798
chr111218048612181685E067-37518
chr111218169612181993E067-37210
chr111218277012183624E067-35579
chr111218423812184292E067-34911
chr111218433812184437E067-34766
chr111218457512184648E067-34555
chr111218474912186425E067-32778
chr111219386612193956E067-25247
chr111219410512194155E067-25048
chr111219419612194307E067-24896
chr111220725212207343E067-11860
chr111220738012208116E067-11087
chr111224132212241703E06722119
chr111224171012242484E06722507
chr111224254012242673E06723337
chr111224269812242895E06723495
chr111224291512243009E06723712
chr111224305912243209E06723856
chr111224353212244417E06724329
chr111226456312266036E06745360
chr111226622612266276E06747023
chr111226645912266639E06747256
chr111226664912266912E06747446
chr111226704612267096E06747843
chr111226716912267983E06747966
chr111226799312268080E06748790
chr111226810812268188E06748905
chr111226825112268331E06749048
chr111226889912269035E06749696
chr111217852812178679E068-40524
chr111217871912179581E068-39622
chr111218020012180405E068-38798
chr111218048612181685E068-37518
chr111218169612181993E068-37210
chr111218474912186425E068-32778
chr111223740112239151E06818198
chr111224171012242484E06822507
chr111224254012242673E06823337
chr111224269812242895E06823495
chr111224291512243009E06823712
chr111224305912243209E06823856
chr111226889912269035E06849696
chr111217215912173201E069-46002
chr111217803712178077E069-41126
chr111217811912178519E069-40684
chr111217852812178679E069-40524
chr111217871912179581E069-39622
chr111217961812179754E069-39449
chr111217981612179919E069-39284
chr111217995612180006E069-39197
chr111218020012180405E069-38798
chr111218048612181685E069-37518
chr111218169612181993E069-37210
chr111218209712182181E069-37022
chr111218225212182622E069-36581
chr111218457512184648E069-34555
chr111218474912186425E069-32778
chr111219220112192286E069-26917
chr111219250412193134E069-26069
chr111223740112239151E06918198
chr111224171012242484E06922507
chr111224254012242673E06923337
chr111224269812242895E06923495
chr111224291512243009E06923712
chr111224305912243209E06923856
chr111224353212244417E06924329
chr111225700712258546E06937804
chr111226456312266036E06945360
chr111226622612266276E06947023
chr111226645912266639E06947256
chr111226664912266912E06947446
chr111226704612267096E06947843
chr111226716912267983E06947966
chr111226799312268080E06948790
chr111226810812268188E06948905
chr111226825112268331E06949048
chr111226889912269035E06949696
chr111218169612181993E070-37210
chr111218209712182181E070-37022
chr111218225212182622E070-36581
chr111224171012242484E07022507
chr111224254012242673E07023337
chr111224269812242895E07023495
chr111224291512243009E07023712
chr111226262812262925E07043425
chr111226303312263233E07043830
chr111226326212263386E07044059
chr111226342912264261E07044226
chr111226430312264389E07045100
chr111226456312266036E07045360
chr111226622612266276E07047023
chr111226645912266639E07047256
chr111226664912266912E07047446
chr111226704612267096E07047843
chr111226716912267983E07047966
chr111217811912178519E071-40684
chr111217852812178679E071-40524
chr111218020012180405E071-38798
chr111218048612181685E071-37518
chr111218169612181993E071-37210
chr111218209712182181E071-37022
chr111218225212182622E071-36581
chr111218277012183624E071-35579
chr111218474912186425E071-32778
chr111219250412193134E071-26069
chr111220376812205291E071-13912
chr111223740112239151E07118198
chr111224171012242484E07122507
chr111224254012242673E07123337
chr111224269812242895E07123495
chr111224291512243009E07123712
chr111224305912243209E07123856
chr111224353212244417E07124329
chr111224508412246723E07125881
chr111226456312266036E07145360
chr111226622612266276E07147023
chr111226645912266639E07147256
chr111226664912266912E07147446
chr111226704612267096E07147843
chr111226716912267983E07147966
chr111226799312268080E07148790
chr111226810812268188E07148905
chr111226825112268331E07149048
chr111226889912269035E07149696
chr111217021712170345E072-48858
chr111217038512170456E072-48747
chr111217070312171066E072-48137
chr111217106912171848E072-47355
chr111217787412177933E072-41270
chr111217803712178077E072-41126
chr111217811912178519E072-40684
chr111217852812178679E072-40524
chr111218169612181993E072-37210
chr111218209712182181E072-37022
chr111218225212182622E072-36581
chr111218277012183624E072-35579
chr111218367212183994E072-35209
chr111218423812184292E072-34911
chr111218433812184437E072-34766
chr111218457512184648E072-34555
chr111218474912186425E072-32778
chr111218675512187302E072-31901
chr111219220112192286E072-26917
chr111219250412193134E072-26069
chr111224171012242484E07222507
chr111224254012242673E07223337
chr111224269812242895E07223495
chr111224291512243009E07223712
chr111224305912243209E07223856
chr111224353212244417E07224329
chr111226456312266036E07245360
chr111226622612266276E07247023
chr111226645912266639E07247256
chr111226664912266912E07247446
chr111226704612267096E07247843
chr111226716912267983E07247966
chr111226799312268080E07248790
chr111226810812268188E07248905
chr111226825112268331E07249048
chr111226889912269035E07249696
chr111217070312171066E073-48137
chr111217106912171848E073-47355
chr111217322512173287E073-45916
chr111217338512173465E073-45738
chr111217756612177616E073-41587
chr111217787412177933E073-41270
chr111217803712178077E073-41126
chr111217811912178519E073-40684
chr111217852812178679E073-40524
chr111218020012180405E073-38798
chr111218048612181685E073-37518
chr111218169612181993E073-37210
chr111218209712182181E073-37022
chr111218225212182622E073-36581
chr111218277012183624E073-35579
chr111218367212183994E073-35209
chr111218423812184292E073-34911
chr111218433812184437E073-34766
chr111218457512184648E073-34555
chr111218474912186425E073-32778
chr111218675512187302E073-31901
chr111220037912200436E073-18767
chr111220046512201834E073-17369
chr111220664812206750E073-12453
chr111220675312206860E073-12343
chr111220690412206989E073-12214
chr111220700512207163E073-12040
chr111220725212207343E073-11860
chr111220738012208116E073-11087
chr111220817012208220E073-10983
chr111222008112220161E073878
chr111224171012242484E07322507
chr111224254012242673E07323337
chr111224269812242895E07323495
chr111224291512243009E07323712
chr111224305912243209E07323856
chr111224353212244417E07324329
chr111225426112254880E07335058
chr111225489312255164E07335690
chr111225678812256952E07337585
chr111225700712258546E07337804
chr111226342912264261E07344226
chr111226430312264389E07345100
chr111226456312266036E07345360
chr111226622612266276E07347023
chr111226645912266639E07347256
chr111226664912266912E07347446
chr111226704612267096E07347843
chr111226889912269035E07349696
chr111218020012180405E074-38798
chr111218048612181685E074-37518
chr111218169612181993E074-37210
chr111218209712182181E074-37022
chr111218225212182622E074-36581
chr111218277012183624E074-35579
chr111218423812184292E074-34911
chr111218433812184437E074-34766
chr111218457512184648E074-34555
chr111218474912186425E074-32778
chr111219220112192286E074-26917
chr111224171012242484E07422507
chr111224254012242673E07423337
chr111224269812242895E07423495
chr111224291512243009E07423712
chr111224305912243209E07423856
chr111224353212244417E07424329
chr111226810812268188E07448905
chr111226889912269035E07449696
chr111218020012180405E081-38798
chr111218048612181685E081-37518
chr111218169612181993E081-37210
chr111218209712182181E081-37022
chr111218225212182622E081-36581
chr111218675512187302E081-31901
chr111218961512189763E081-29440
chr111218979512189958E081-29245
chr111223541612235529E08116213
chr111223555012235903E08116347
chr111223593112236032E08116728
chr111223625912237378E08117056
chr111223740112239151E08118198
chr111223918212239397E08119979
chr111223949112239572E08120288
chr111223963412239720E08120431
chr111223982112240012E08120618
chr111224011812240168E08120915
chr111224024912240349E08121046
chr111224042612240940E08121223
chr111224107612241249E08121873
chr111224132212241703E08122119
chr111224171012242484E08122507
chr111224254012242673E08123337
chr111224269812242895E08123495
chr111224291512243009E08123712
chr111224305912243209E08123856
chr111225574312255815E08136540
chr111225589712256093E08136694
chr111225610512256453E08136902
chr111225678812256952E08137585
chr111226342912264261E08144226
chr111226430312264389E08145100
chr111226456312266036E08145360
chr111226622612266276E08147023
chr111226645912266639E08147256
chr111226664912266912E08147446
chr111226704612267096E08147843
chr111226716912267983E08147966
chr111226799312268080E08148790
chr111226810812268188E08148905
chr111218048612181685E082-37518
chr111218169612181993E082-37210
chr111223625912237378E08217056
chr111223740112239151E08218198
chr111223918212239397E08219979
chr111224132212241703E08222119
chr111224171012242484E08222507
chr111226342912264261E08244226
chr111226430312264389E08245100
chr111226456312266036E08245360
chr111226622612266276E08247023
chr111226645912266639E08247256
chr111226664912266912E08247446
chr111226704612267096E08247843
chr111226716912267983E08247966