rs6664668

Homo sapiens
G>A
H3F3A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0043 (1309/29982,GnomAD)
G==0072 (2121/29116,TOPMED)
G==0046 (230/5008,1000G)
G==0001 (4/3854,ALSPAC)
G==0000 (1/3708,TWINSUK)
chr1:226068253 (GRCh38.p7) (1q42.12)
ND
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.226068253G>A
GRCh37.p13 chr 1NC_000001.10:g.226255954G>A

Gene: H3F3A, H3 histone, family 3A(plus strand)

Molecule type Change Amino acid[Codon] SO Term
H3F3A transcriptNM_002107.4:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.158A=0.842
1000GenomesAmericanSub694G=0.030A=0.970
1000GenomesEast AsianSub1008G=0.000A=1.000
1000GenomesEuropeSub1006G=0.001A=0.999
1000GenomesGlobalStudy-wide5008G=0.046A=0.954
1000GenomesSouth AsianSub978G=0.000A=1.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.001A=0.999
The Genome Aggregation DatabaseAfricanSub8724G=0.149A=0.851
The Genome Aggregation DatabaseAmericanSub838G=0.000A=1.000
The Genome Aggregation DatabaseEast AsianSub1618G=0.000A=1.000
The Genome Aggregation DatabaseEuropeSub18500G=0.000A=0.999
The Genome Aggregation DatabaseGlobalStudy-wide29982G=0.043A=0.956
The Genome Aggregation DatabaseOtherSub302G=0.000A=1.000
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.072A=0.927
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.000A=1.000
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs66646686.96E-06alcohol and nictotine co-dependence20158304

eQTL of rs6664668 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 rs6664668 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 )
chr1226222099226222633E067-33321
chr1226254013226254068E067-1886
chr1226254081226254165E067-1789
chr1226254313226254661E067-1293
chr1226300053226300103E06744099
chr1226300241226300445E06744287
chr1226222099226222633E068-33321
chr1226254013226254068E068-1886
chr1226254081226254165E068-1789
chr1226254313226254661E068-1293
chr1226256040226256119E06886
chr1226296749226296996E06840795
chr1226300053226300103E06844099
chr1226300241226300445E06844287
chr1226222099226222633E069-33321
chr1226254313226254661E069-1293
chr1226254697226254741E069-1213
chr1226254821226254871E069-1083
chr1226300053226300103E06944099
chr1226300241226300445E06944287
chr1226248373226248493E070-7461
chr1226287766226287821E07031812
chr1226287837226287892E07031883
chr1226296749226296996E07040795
chr1226300053226300103E07044099
chr1226300241226300445E07044287
chr1226235262226235511E071-20443
chr1226254013226254068E071-1886
chr1226254081226254165E071-1789
chr1226254313226254661E071-1293
chr1226254697226254741E071-1213
chr1226254821226254871E071-1083
chr1226287766226287821E07131812
chr1226296749226296996E07140795
chr1226300053226300103E07144099
chr1226222099226222633E072-33321
chr1226254013226254068E072-1886
chr1226254081226254165E072-1789
chr1226254313226254661E072-1293
chr1226254697226254741E072-1213
chr1226254821226254871E072-1083
chr1226296749226296996E07240795
chr1226242746226242836E073-13118
chr1226254013226254068E073-1886
chr1226254081226254165E073-1789
chr1226254313226254661E073-1293
chr1226300053226300103E07344099
chr1226222099226222633E074-33321
chr1226254013226254068E074-1886
chr1226254081226254165E074-1789
chr1226287766226287821E07431812
chr1226287837226287892E07431883
chr1226296749226296996E07440795
chr1226222099226222633E081-33321
chr1226222099226222633E082-33321
chr1226242369226242508E082-13446
chr1226242746226242836E082-13118
chr1226248373226248493E082-7461
chr1226300053226300103E08244099
chr1226300241226300445E08244287










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1226248729226252065E067-3889
chr1226252142226252450E067-3504
chr1226252494226252929E067-3025
chr1226270605226271897E06714651
chr1226288151226288252E06732197
chr1226288314226288518E06732360
chr1226288593226289075E06732639
chr1226297086226299919E06741132
chr1226248729226252065E068-3889
chr1226252142226252450E068-3504
chr1226252494226252929E068-3025
chr1226270605226271897E06814651
chr1226288151226288252E06832197
chr1226288314226288518E06832360
chr1226288593226289075E06832639
chr1226297086226299919E06841132
chr1226248729226252065E069-3889
chr1226252142226252450E069-3504
chr1226252494226252929E069-3025
chr1226270605226271897E06914651
chr1226288151226288252E06932197
chr1226288314226288518E06932360
chr1226288593226289075E06932639
chr1226297086226299919E06941132
chr1226248729226252065E070-3889
chr1226252142226252450E070-3504
chr1226252494226252929E070-3025
chr1226270605226271897E07014651
chr1226288314226288518E07032360
chr1226297086226299919E07041132
chr1226248729226252065E071-3889
chr1226252142226252450E071-3504
chr1226252494226252929E071-3025
chr1226270605226271897E07114651
chr1226288151226288252E07132197
chr1226288314226288518E07132360
chr1226288593226289075E07132639
chr1226297086226299919E07141132
chr1226248729226252065E072-3889
chr1226252142226252450E072-3504
chr1226252494226252929E072-3025
chr1226270605226271897E07214651
chr1226288151226288252E07232197
chr1226288314226288518E07232360
chr1226288593226289075E07232639
chr1226297086226299919E07241132
chr1226248729226252065E073-3889
chr1226252142226252450E073-3504
chr1226252494226252929E073-3025
chr1226270605226271897E07314651
chr1226288151226288252E07332197
chr1226288314226288518E07332360
chr1226288593226289075E07332639
chr1226297086226299919E07341132
chr1226248729226252065E074-3889
chr1226252142226252450E074-3504
chr1226252494226252929E074-3025
chr1226270605226271897E07414651
chr1226288151226288252E07432197
chr1226288314226288518E07432360
chr1226297086226299919E07441132
chr1226252142226252450E081-3504
chr1226252494226252929E081-3025
chr1226248729226252065E082-3889
chr1226252142226252450E082-3504
chr1226252494226252929E082-3025
chr1226270605226271897E08214651
chr1226288151226288252E08232197
chr1226288314226288518E08232360
chr1226288593226289075E08232639
chr1226297086226299919E08241132