rs3020213

Homo sapiens
C>T
MCPH1 : Intron Variant
ANGPT2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0362 (10843/29914,GnomAD)
T=0370 (10777/29118,TOPMED)
T=0329 (1648/5008,1000G)
T=0400 (1540/3854,ALSPAC)
T=0398 (1475/3708,TWINSUK)
chr8:6512409 (GRCh38.p7) (8p23.1)
ND
GWASdb2
1   publication(s)
See rs on genome
115 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.6512409C>T
GRCh37.p13 chr 8NC_000008.10:g.6369930C>T
MCPH1 RefSeqGeneNG_016619.2:g.110818C>T
ANGPT2 RefSeqGeneNG_029483.1:g.55855G>A

Gene: ANGPT2, angiopoietin 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ANGPT2 transcript variant 2NM_001118887.1:c.N/AIntron Variant
ANGPT2 transcript variant 3NM_001118888.1:c.N/AIntron Variant
ANGPT2 transcript variant 1NM_001147.2:c.N/AIntron Variant
ANGPT2 transcript variant X1XM_017013318.1:c.N/AIntron Variant

Gene: MCPH1, microcephalin 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MCPH1 transcript variant 4NM_001322042.1:c.N/AIntron Variant
MCPH1 transcript variant 1NM_024596.4:c.N/AIntron Variant
MCPH1 transcript variant 2NM_001172574.1:c.N/AGenic Downstream Transcript Variant
MCPH1 transcript variant 3NM_001172575.1:c.N/AGenic Downstream Transcript Variant
MCPH1 transcript variant 5NM_001322043.1:c.N/AGenic Downstream Transcript Variant
MCPH1 transcript variant 6NM_001322045.1:c.N/AGenic Downstream Transcript Variant
MCPH1 transcript variant 7NR_136159.1:n.N/AGenic Downstream Transcript Variant
MCPH1 transcript variant X2XM_011534755.2:c.N/AIntron Variant
MCPH1 transcript variant X7XM_011534756.2:c.N/AIntron Variant
MCPH1 transcript variant X8XM_011534757.2:c.N/AIntron Variant
MCPH1 transcript variant X11XM_011534759.2:c.N/AIntron Variant
MCPH1 transcript variant X13XM_011534760.2:c.N/AIntron Variant
MCPH1 transcript variant X1XM_017013829.1:c.N/AIntron Variant
MCPH1 transcript variant X3XM_017013830.1:c.N/AIntron Variant
MCPH1 transcript variant X5XM_017013831.1:c.N/AIntron Variant
MCPH1 transcript variant X6XM_017013832.1:c.N/AIntron Variant
MCPH1 transcript variant X9XM_017013833.1:c.N/AIntron Variant
MCPH1 transcript variant X12XM_017013834.1:c.N/AIntron Variant
MCPH1 transcript variant X10XM_011534758.2:c.N/A3 Prime UTR Variant
MCPH1 transcript variant X4XR_001745596.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.630T=0.370
1000GenomesAmericanSub694C=0.710T=0.290
1000GenomesEast AsianSub1008C=0.785T=0.215
1000GenomesEuropeSub1006C=0.602T=0.398
1000GenomesGlobalStudy-wide5008C=0.671T=0.329
1000GenomesSouth AsianSub978C=0.650T=0.350
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.600T=0.400
The Genome Aggregation DatabaseAfricanSub8718C=0.621T=0.379
The Genome Aggregation DatabaseAmericanSub836C=0.730T=0.270
The Genome Aggregation DatabaseEast AsianSub1612C=0.783T=0.217
The Genome Aggregation DatabaseEuropeSub18446C=0.629T=0.371
The Genome Aggregation DatabaseGlobalStudy-wide29914C=0.637T=0.362
The Genome Aggregation DatabaseOtherSub302C=0.580T=0.420
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.629T=0.370
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.602T=0.398
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs30202130.000847nicotine smoking19268276

eQTL of rs3020213 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 rs3020213 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 )
chr863751356375205E0675205
chr863753196375386E0675389
chr863764676376628E0676537
chr863767396376779E0676809
chr863772146377299E0677284
chr863773186377446E0677388
chr863211096321197E068-48733
chr863212326321942E068-47988
chr863419106342492E068-27438
chr863727396373003E0682809
chr863730466373114E0683116
chr863732896373602E0683359
chr863773186377446E0687388
chr863860376386392E06816107
chr864041696405777E06834239
chr863206306320690E069-49240
chr863207356321027E069-48903
chr863211096321197E069-48733
chr863212326321942E069-47988
chr863722226372371E0692292
chr863726696372734E0692739
chr863727396373003E0692809
chr863730466373114E0693116
chr863732896373602E0693359
chr863751356375205E0695205
chr863753196375386E0695389
chr863764676376628E0696537
chr863767396376779E0696809
chr863772146377299E0697284
chr863773186377446E0697388
chr863212326321942E070-47988
chr863220116322077E070-47853
chr863224366322499E070-47431
chr863226276322782E070-47148
chr863772146377299E0707284
chr863773186377446E0707388
chr864074826408186E07037552
chr864082306408532E07038300
chr864085936408716E07038663
chr864087776408910E07038847
chr864089636409015E07039033
chr863206306320690E071-49240
chr863207356321027E071-48903
chr863211096321197E071-48733
chr863212326321942E071-47988
chr863220116322077E071-47853
chr863326066332756E071-37174
chr863329906333055E071-36875
chr863432316343480E071-26450
chr863726696372734E0712739
chr863727396373003E0712809
chr863730466373114E0713116
chr863732896373602E0713359
chr863738276374531E0713897
chr863751356375205E0715205
chr863753196375386E0715389
chr863764676376628E0716537
chr863767396376779E0716809
chr863772146377299E0717284
chr863773186377446E0717388
chr863882026388252E07118272
chr863898056390471E07119875
chr863960386396092E07126108
chr863962746396324E07126344
chr863979506398087E07128020
chr863981666398494E07128236
chr863986006398745E07128670
chr863988116398903E07128881
chr863989146399114E07128984
chr863206306320690E072-49240
chr863207356321027E072-48903
chr863211096321197E072-48733
chr863212326321942E072-47988
chr863419106342492E072-27438
chr863751356375205E0725205
chr863753196375386E0725389
chr863764676376628E0726537
chr863767396376779E0726809
chr863772146377299E0727284
chr863773186377446E0727388
chr863860376386392E07216107
chr863891266389528E07219196
chr863895586389638E07219628
chr863898056390471E07219875
chr863211096321197E073-48733
chr863212326321942E073-47988
chr863220116322077E073-47853
chr863726696372734E0732739
chr863727396373003E0732809
chr863730466373114E0733116
chr863732896373602E0733359
chr863772146377299E0737284
chr863773186377446E0737388
chr864022796402397E07332349
chr863200216320080E074-49850
chr863202706320310E074-49620
chr863204276320528E074-49402
chr863206306320690E074-49240
chr863207356321027E074-48903
chr863211096321197E074-48733
chr863212326321942E074-47988
chr863419106342492E074-27438
chr863751356375205E0745205
chr863753196375386E0745389
chr863764676376628E0746537
chr863767396376779E0746809
chr863772146377299E0747284
chr863773186377446E0747388
chr863891266389528E07419196
chr863895586389638E07419628
chr863898056390471E07419875
chr864178196419149E07447889
chr863979506398087E08128020
chr863981666398494E08128236
chr863999186399968E08129988