rs6028335

Homo sapiens
A>G
LOC107985448 : Intron Variant
LOC339568 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0162 (4879/29954,GnomAD)
G=0149 (4343/29118,TOPMED)
G=0140 (700/5008,1000G)
G=0203 (784/3854,ALSPAC)
G=0211 (782/3708,TWINSUK)
chr20:39216834 (GRCh38.p7) (20q12)
ND
GWASdb2 | GWASCatalog
1   publication(s)
See rs on genome
24 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.39216834A>G
GRCh37.p13 chr 20NC_000020.10:g.37845477A>G

Gene: LOC339568, uncharacterized LOC339568(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01734 transcriptNR_027124.1:n.N/AIntron Variant

Gene: LOC107985448, uncharacterized LOC107985448(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107985448 transcriptXR_001754587.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.973G=0.027
1000GenomesAmericanSub694A=0.820G=0.180
1000GenomesEast AsianSub1008A=0.918G=0.082
1000GenomesEuropeSub1006A=0.746G=0.254
1000GenomesGlobalStudy-wide5008A=0.860G=0.140
1000GenomesSouth AsianSub978A=0.800G=0.200
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.797G=0.203
The Genome Aggregation DatabaseAfricanSub8724A=0.943G=0.057
The Genome Aggregation DatabaseAmericanSub838A=0.830G=0.170
The Genome Aggregation DatabaseEast AsianSub1618A=0.896G=0.104
The Genome Aggregation DatabaseEuropeSub18474A=0.784G=0.215
The Genome Aggregation DatabaseGlobalStudy-wide29954A=0.837G=0.162
The Genome Aggregation DatabaseOtherSub300A=0.720G=0.280
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.850G=0.149
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.789G=0.211
PMID Title Author Journal
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs60283355E-06alcohol and nicotine co-dependence22488850

eQTL of rs6028335 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 rs6028335 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 )
chr203780461737804667E070-40810
chr203780466837804718E070-40759
chr203780518037805313E070-40164
chr203783901337839063E070-6414
chr203783908637839703E070-5774
chr203783989837839938E070-5539
chr203784339537844154E070-1323
chr203788767237888056E07042195
chr203788869737888747E07043220
chr203782420437824469E081-21008
chr203782448637824673E081-20804
chr203783901337839063E081-6414
chr203783908637839703E081-5774
chr203784339537844154E081-1323
chr203788767237888056E08142195
chr203788869737888747E08143220
chr203789459137894757E08149114
chr203789484437894906E08149367
chr203784339537844154E082-1323
chr203788767237888056E08242195
chr203789313837893571E08247661
chr203789361937893691E08248142
chr203789389137893935E08248414
chr203789416237894281E08248685