rs116478358

Homo sapiens
T>A
APBB2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0006 (181/29990,GnomAD)
A=0011 (329/29118,TOPMED)
A=0012 (59/5008,1000G)
A=0000 (0/3854,ALSPAC)
A=0000 (1/3708,TWINSUK)
chr4:40826202 (GRCh38.p7) (4p14)
CD
GWASdb2
1   publication(s)
See rs on genome
189 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.40826202T>A
GRCh37.p13 chr 4NC_000004.11:g.40828219T>A
APBB2 RefSeqGeneNG_013337.1:g.393417A>T

Gene: APBB2, amyloid beta precursor protein binding family B member 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
APBB2 transcript variant 2NM_001166050.1:c.N/AIntron Variant
APBB2 transcript variant 4NM_001166051.1:c.N/AIntron Variant
APBB2 transcript variant 5NM_001166052.1:c.N/AIntron Variant
APBB2 transcript variant 6NM_001166053.1:c.N/AIntron Variant
APBB2 transcript variant 7NM_001166054.1:c.N/AIntron Variant
APBB2 transcript variant 1NM_004307.1:c.N/AIntron Variant
APBB2 transcript variant 3NM_173075.4:c.N/AIntron Variant
APBB2 transcript variant X23XM_005248101.3:c.N/AIntron Variant
APBB2 transcript variant X1XM_006714005.3:c.N/AIntron Variant
APBB2 transcript variant X3XM_006714007.3:c.N/AIntron Variant
APBB2 transcript variant X5XM_006714008.3:c.N/AIntron Variant
APBB2 transcript variant X6XM_006714009.3:c.N/AIntron Variant
APBB2 transcript variant X7XM_006714010.3:c.N/AIntron Variant
APBB2 transcript variant X15XM_006714011.3:c.N/AIntron Variant
APBB2 transcript variant X18XM_006714012.3:c.N/AIntron Variant
APBB2 transcript variant X4XM_011513686.2:c.N/AIntron Variant
APBB2 transcript variant X20XM_011513687.2:c.N/AIntron Variant
APBB2 transcript variant X2XM_017008142.1:c.N/AIntron Variant
APBB2 transcript variant X8XM_017008143.1:c.N/AIntron Variant
APBB2 transcript variant X9XM_017008144.1:c.N/AIntron Variant
APBB2 transcript variant X10XM_017008145.1:c.N/AIntron Variant
APBB2 transcript variant X11XM_017008146.1:c.N/AIntron Variant
APBB2 transcript variant X12XM_017008147.1:c.N/AIntron Variant
APBB2 transcript variant X13XM_017008148.1:c.N/AIntron Variant
APBB2 transcript variant X14XM_017008149.1:c.N/AIntron Variant
APBB2 transcript variant X16XM_017008150.1:c.N/AIntron Variant
APBB2 transcript variant X17XM_017008151.1:c.N/AIntron Variant
APBB2 transcript variant X19XM_017008152.1:c.N/AIntron Variant
APBB2 transcript variant X21XM_017008153.1:c.N/AIntron Variant
APBB2 transcript variant X22XM_017008154.1:c.N/AIntron Variant
APBB2 transcript variant X24XM_017008155.1:c.N/AIntron Variant
APBB2 transcript variant X25XM_017008156.1:c.N/AIntron Variant
APBB2 transcript variant X26XM_017008157.1:c.N/AIntron Variant
APBB2 transcript variant X27XM_017008158.1:c.N/AIntron Variant
APBB2 transcript variant X28XM_011513688.2:c.N/AGenic Downstream Transcript Variant
APBB2 transcript variant X29XM_017008159.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.958A=0.042
1000GenomesAmericanSub694T=1.000A=0.000
1000GenomesEast AsianSub1008T=1.000A=0.000
1000GenomesEuropeSub1006T=0.999A=0.001
1000GenomesGlobalStudy-wide5008T=0.988A=0.012
1000GenomesSouth AsianSub978T=1.000A=0.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=1.000A=0.000
The Genome Aggregation DatabaseAfricanSub8730T=0.979A=0.021
The Genome Aggregation DatabaseAmericanSub838T=1.000A=0.000
The Genome Aggregation DatabaseEast AsianSub1622T=1.000A=0.000
The Genome Aggregation DatabaseEuropeSub18498T=1.000A=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29990T=0.994A=0.006
The Genome Aggregation DatabaseOtherSub302T=1.000A=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.988A=0.011
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=1.000A=0.000
PMID Title Author Journal
23958962Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.Gelernter JMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs1164783582.08E-05cocaine dependence23958962

eQTL of rs116478358 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 rs116478358 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 )
chr44081426240814457E067-13762
chr44081459240814760E067-13459
chr44083357640833920E0675357
chr44083912340839299E06710904
chr44083935240839402E06711133
chr44083961140839752E06711392
chr44084299740843510E06714778
chr44084376040843897E06715541
chr44084428540844781E06716066
chr44084479940844923E06716580
chr44084495440845433E06716735
chr44084576240846055E06717543
chr44084659240846686E06718373
chr44084727840847543E06719059
chr44084763640847904E06719417
chr44084863540848810E06720416
chr44085030740850586E06722088
chr44085070740851212E06722488
chr44085300840853065E06724789
chr44085782740857887E06729608
chr44086110640861299E06732887
chr44087698540877181E06748766
chr44079049240790586E068-37633
chr44081426240814457E068-13762
chr44081459240814760E068-13459
chr44083357640833920E0685357
chr44083912340839299E06810904
chr44083935240839402E06811133
chr44083961140839752E06811392
chr44084217340842784E06813954
chr44084299740843510E06814778
chr44084376040843897E06815541
chr44084495440845433E06816735
chr44084576240846055E06817543
chr44084659240846686E06818373
chr44084727840847543E06819059
chr44084763640847904E06819417
chr44084863540848810E06820416
chr44085030740850586E06822088
chr44085070740851212E06822488
chr44085265640852772E06824437
chr44085300840853065E06824789
chr44085365040853729E06825431
chr44086007640860340E06831857
chr44086110640861299E06832887
chr44087698540877181E06848766
chr44079049240790586E069-37633
chr44081426240814457E069-13762
chr44081459240814760E069-13459
chr44083357640833920E0695357
chr44083901840839078E06910799
chr44083912340839299E06910904
chr44083935240839402E06911133
chr44083961140839752E06911392
chr44084217340842784E06913954
chr44084299740843510E06914778
chr44084376040843897E06915541
chr44084495440845433E06916735
chr44084576240846055E06917543
chr44084659240846686E06918373
chr44084727840847543E06919059
chr44084763640847904E06919417
chr44084863540848810E06920416
chr44085030740850586E06922088
chr44085070740851212E06922488
chr44085265640852772E06924437
chr44085300840853065E06924789
chr44085365040853729E06925431
chr44085782740857887E06929608
chr44086007640860340E06931857
chr44086110640861299E06932887
chr44087648840876668E06948269
chr44087698540877181E06948766
chr44087765640878103E06949437
chr44082028240820347E070-7872
chr44083357640833920E0705357
chr44083912340839299E07010904
chr44083935240839402E07011133
chr44083961140839752E07011392
chr44084376040843897E07015541
chr44084576240846055E07017543
chr44084659240846686E07018373
chr44084727840847543E07019059
chr44084763640847904E07019417
chr44084863540848810E07020416
chr44085265640852772E07024437
chr44085300840853065E07024789
chr44087648840876668E07048269
chr44087698540877181E07048766
chr44079049240790586E071-37633
chr44083357640833920E0715357
chr44083901840839078E07110799
chr44083912340839299E07110904
chr44083935240839402E07111133
chr44083961140839752E07111392
chr44084495440845433E07116735
chr44084576240846055E07117543
chr44084659240846686E07118373
chr44084727840847543E07119059
chr44084763640847904E07119417
chr44085030740850586E07122088
chr44085070740851212E07122488
chr44085265640852772E07124437
chr44085300840853065E07124789
chr44085365040853729E07125431
chr44085782740857887E07129608
chr44086007640860340E07131857
chr44086110640861299E07132887
chr44087648840876668E07148269
chr44087698540877181E07148766
chr44079049240790586E072-37633
chr44081459240814760E072-13459
chr44082715040827467E072-752
chr44083357640833920E0725357
chr44083901840839078E07210799
chr44083912340839299E07210904
chr44083935240839402E07211133
chr44084299740843510E07214778
chr44084376040843897E07215541
chr44084428540844781E07216066
chr44084479940844923E07216580
chr44084495440845433E07216735
chr44084576240846055E07217543
chr44084727840847543E07219059
chr44084763640847904E07219417
chr44084863540848810E07220416
chr44085030740850586E07222088
chr44085070740851212E07222488
chr44085265640852772E07224437
chr44085300840853065E07224789
chr44085365040853729E07225431
chr44086007640860340E07231857
chr44086110640861299E07232887
chr44081426240814457E073-13762
chr44081459240814760E073-13459
chr44083901840839078E07310799
chr44083912340839299E07310904
chr44083935240839402E07311133
chr44083961140839752E07311392
chr44084495440845433E07316735
chr44084576240846055E07317543
chr44084659240846686E07318373
chr44084727840847543E07319059
chr44084763640847904E07319417
chr44085030740850586E07322088
chr44085070740851212E07322488
chr44086110640861299E07332887
chr44079110540791271E074-36948
chr44081426240814457E074-13762
chr44081459240814760E074-13459
chr44083901840839078E07410799
chr44083912340839299E07410904
chr44083935240839402E07411133
chr44083961140839752E07411392
chr44084217340842784E07413954
chr44084299740843510E07414778
chr44084376040843897E07415541
chr44084428540844781E07416066
chr44084479940844923E07416580
chr44084495440845433E07416735
chr44084576240846055E07417543
chr44084659240846686E07418373
chr44084727840847543E07419059
chr44084763640847904E07419417
chr44084863540848810E07420416
chr44085030740850586E07422088
chr44085070740851212E07422488
chr44085265640852772E07424437
chr44085300840853065E07424789
chr44086007640860340E07431857
chr44086110640861299E07432887
chr44087648840876668E07448269
chr44087698540877181E07448766
chr44083357640833920E0815357
chr44083912340839299E08110904
chr44083935240839402E08111133
chr44083961140839752E08111392
chr44084495440845433E08116735
chr44084659240846686E08118373
chr44084727840847543E08119059
chr44084763640847904E08119417
chr44085030740850586E08122088
chr44085070740851212E08122488
chr44083901840839078E08210799
chr44083912340839299E08210904
chr44083935240839402E08211133
chr44084727840847543E08219059
chr44084763640847904E08219417
chr44086110640861299E08232887










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr44085886240859472E06730643
chr44085805740858170E06829838
chr44085817340858559E06829954
chr44085886240859472E06830643
chr44085886240859472E06930643
chr44085805740858170E07029838
chr44085817340858559E07029954
chr44085886240859472E07030643
chr44085805740858170E07129838
chr44085817340858559E07129954
chr44085886240859472E07130643
chr44085817340858559E07229954
chr44085886240859472E07230643
chr44085886240859472E07330643
chr44085886240859472E07430643
chr44085805740858170E08129838
chr44085817340858559E08129954
chr44085805740858170E08229838
chr44085817340858559E08229954
chr44085886240859472E08230643