rs4889294

Homo sapiens
T>C
BCO1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0358 (43476/121370,ExAC)
C=0325 (9727/29876,GnomAD)
C=0274 (7997/29118,TOPMED)
T==0338 (4396/13004,GO-ESP)
C=0213 (1067/5008,1000G)
C=0445 (1716/3854,ALSPAC)
C=0455 (1688/3708,TWINSUK)
chr16:81270154 (GRCh38.p7) (16q23.2)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.81270154T>C
GRCh37.p13 chr 16NC_000016.9:g.81303759T>C
BCO1 RefSeqGeneNG_012171.1:g.36464T>C

Gene: BCO1, beta-carotene oxygenase 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
BCO1 transcriptNM_017429.2:c.N/AIntron Variant
BCO1 transcript variant X1XM_011523109.1:c.N/AIntron Variant
BCO1 transcript variant X2XM_017023286.1:c.N/AIntron Variant
BCO1 transcript variant X3XM_017023287.1:c.N/AIntron Variant
BCO1 transcript variant X4XM_017023288.1:c.N/AIntron Variant
BCO1 transcript variant X5XM_017023289.1:c.N/AIntron Variant
BCO1 transcript variant X6XR_001751914.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.978C=0.022
1000GenomesAmericanSub694T=0.680C=0.320
1000GenomesEast AsianSub1008T=0.865C=0.135
1000GenomesEuropeSub1006T=0.553C=0.447
1000GenomesGlobalStudy-wide5008T=0.787C=0.213
1000GenomesSouth AsianSub978T=0.770C=0.230
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.555C=0.445
The Exome Aggregation ConsortiumAmericanSub21972T=0.805C=0.194
The Exome Aggregation ConsortiumAsianSub25150T=0.776C=0.223
The Exome Aggregation ConsortiumEuropeSub73340T=0.547C=0.452
The Exome Aggregation ConsortiumGlobalStudy-wide121370T=0.641C=0.358
The Exome Aggregation ConsortiumOtherSub908T=0.580C=0.420
The Genome Aggregation DatabaseAfricanSub8688T=0.910C=0.090
The Genome Aggregation DatabaseAmericanSub836T=0.680C=0.320
The Genome Aggregation DatabaseEast AsianSub1616T=0.860C=0.140
The Genome Aggregation DatabaseEuropeSub18434T=0.549C=0.450
The Genome Aggregation DatabaseGlobalStudy-wide29876T=0.674C=0.325
The Genome Aggregation DatabaseOtherSub302T=0.530C=0.470
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.725C=0.274
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.545C=0.455
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs48892940.000203alcohol consumption (maxi-drinks)24277619

eQTL of rs4889294 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 rs4889294 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 )
chr168134535681345458E06741597
chr168134551881345568E06741759
chr168134630181346346E06742542
chr168135016081350215E06746401
chr168135021981350259E06746460
chr168135029981350387E06746540
chr168135041081350482E06746651
chr168135073481350784E06746975
chr168135078881350853E06747029
chr168135090881350965E06747149
chr168135102581351106E06747266
chr168127089181271591E068-32168
chr168127162581271760E068-31999
chr168129967481300127E068-3632
chr168131088181311144E0687122
chr168134639981346449E06842640
chr168135078881350853E06847029
chr168135090881350965E06847149
chr168127089181271591E069-32168
chr168127162581271760E069-31999
chr168134243181342565E06938672
chr168134535681345458E06941597
chr168134551881345568E06941759
chr168134630181346346E06942542
chr168134639981346449E06942640
chr168129951181299561E070-4198
chr168129967481300127E070-3632
chr168134639981346449E07042640
chr168135016081350215E07046401
chr168135041081350482E07046651
chr168135073481350784E07046975
chr168135078881350853E07047029
chr168135090881350965E07047149
chr168135102581351106E07047266
chr168127089181271591E071-32168
chr168127162581271760E071-31999
chr168129703181297982E071-5777
chr168129814881298198E071-5561
chr168129832281298421E071-5338
chr168129951181299561E071-4198
chr168129967481300127E071-3632
chr168130025181300734E071-3025
chr168130850881308785E0714749
chr168130882281308996E0715063
chr168130902081309243E0715261
chr168134526681345316E07141507
chr168134535681345458E07141597
chr168134551881345568E07141759
chr168127089181271591E072-32168
chr168135358281353651E07249823
chr168135370281353757E07249943
chr168129951181299561E073-4198
chr168134526681345316E07341507
chr168134535681345458E07341597
chr168134551881345568E07341759
chr168135016081350215E07346401
chr168135021981350259E07346460
chr168135029981350387E07346540
chr168130653481306588E0742775
chr168134526681345316E07441507
chr168134535681345458E07441597
chr168134551881345568E07441759
chr168134630181346346E07442542
chr168134639981346449E07442640
chr168135197181352060E07448212
chr168135016081350215E08146401
chr168135021981350259E08146460
chr168135029981350387E08146540
chr168135041081350482E08146651
chr168135073481350784E08146975
chr168135078881350853E08147029
chr168134551881345568E08241759










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr168127180181272604E067-31155
chr168134776381349964E06744004
chr168127180181272604E068-31155
chr168134776381349964E06844004
chr168127180181272604E069-31155
chr168134776381349964E06944004
chr168134776381349964E07044004
chr168127180181272604E071-31155
chr168134776381349964E07144004
chr168127180181272604E072-31155
chr168134776381349964E07244004
chr168127180181272604E073-31155
chr168134776381349964E07344004
chr168127180181272604E074-31155
chr168134776381349964E07444004
chr168134776381349964E08244004