rs7322488

Homo sapiens
T>C
HS6ST3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0055 (1656/29960,GnomAD)
C=0047 (1380/29118,TOPMED)
C=0086 (429/5008,1000G)
C=0036 (138/3854,ALSPAC)
C=0035 (128/3708,TWINSUK)
chr13:96264380 (GRCh38.p7) (13q32.1)
ND
GWASdb2
1   publication(s)
See rs on genome
11 Enhancers around
3 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.96264380T>C
GRCh37.p13 chr 13NC_000013.10:g.96916634T>C

Gene: HS6ST3, heparan sulfate 6-O-sulfotransferase 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
HS6ST3 transcriptNM_153456.3:c.N/AIntron Variant
HS6ST3 transcript variant X1XM_011521076.2:c.N/AIntron Variant
HS6ST3 transcript variant X2XM_017020543.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.952C=0.048
1000GenomesAmericanSub694T=0.920C=0.080
1000GenomesEast AsianSub1008T=0.844C=0.156
1000GenomesEuropeSub1006T=0.958C=0.042
1000GenomesGlobalStudy-wide5008T=0.914C=0.086
1000GenomesSouth AsianSub978T=0.880C=0.120
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.964C=0.036
The Genome Aggregation DatabaseAfricanSub8728T=0.953C=0.047
The Genome Aggregation DatabaseAmericanSub838T=0.920C=0.080
The Genome Aggregation DatabaseEast AsianSub1610T=0.842C=0.158
The Genome Aggregation DatabaseEuropeSub18482T=0.952C=0.047
The Genome Aggregation DatabaseGlobalStudy-wide29960T=0.944C=0.055
The Genome Aggregation DatabaseOtherSub302T=0.870C=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.952C=0.047
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.965C=0.035
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
rs73224880.000334nicotine smoking19268276

eQTL of rs7322488 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 rs7322488 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 )
chr139689115596891443E067-25191
chr139687554596875650E068-40984
chr139689115596891443E068-25191
chr139689115596891443E071-25191
chr139689101996891069E072-25565
chr139687988696880141E074-36493
chr139689115596891443E074-25191
chr139696089496961158E08244260
chr139696122896961278E08244594
chr139696192096962035E08245286
chr139696233196962381E08245697






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr139689053196890810E068-25824
chr139689053196890810E069-25824
chr139689053196890810E071-25824