rs2487891

Homo sapiens
T>C
HPSE2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0356 (10612/29748,GnomAD)
T==0408 (11892/29118,TOPMED)
T==0369 (1849/5008,1000G)
T==0216 (832/3854,ALSPAC)
T==0221 (819/3708,TWINSUK)
chr10:99040075 (GRCh38.p7) (10q24.2)
ND
GWASdb2
1   publication(s)
See rs on genome
12 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.99040075T>C
GRCh37.p13 chr 10NC_000010.10:g.100799832T>C
HPSE2 RefSeqGeneNG_023416.1:g.200801A>G

Gene: HPSE2, heparanase 2 (inactive)(minus strand)

Molecule type Change Amino acid[Codon] SO Term
HPSE2 transcript variant 2NM_001166244.1:c.N/AIntron Variant
HPSE2 transcript variant 3NM_001166245.1:c.N/AIntron Variant
HPSE2 transcript variant 4NM_001166246.1:c.N/AIntron Variant
HPSE2 transcript variant 1NM_021828.4:c.N/AIntron Variant
HPSE2 transcript variant X5XM_006717937.2:c.N/AIntron Variant
HPSE2 transcript variant X2XM_011540029.1:c.N/AIntron Variant
HPSE2 transcript variant X3XM_011540030.1:c.N/AIntron Variant
HPSE2 transcript variant X7XM_011540031.2:c.N/AIntron Variant
HPSE2 transcript variant X9XM_011540033.2:c.N/AIntron Variant
HPSE2 transcript variant X1XM_017016495.1:c.N/AIntron Variant
HPSE2 transcript variant X4XM_017016496.1:c.N/AIntron Variant
HPSE2 transcript variant X8XM_017016497.1:c.N/AIntron Variant
HPSE2 transcript variant X11XM_017016498.1:c.N/AIntron Variant
HPSE2 transcript variant X9XR_001747170.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.706C=0.294
1000GenomesAmericanSub694T=0.260C=0.740
1000GenomesEast AsianSub1008T=0.236C=0.764
1000GenomesEuropeSub1006T=0.208C=0.792
1000GenomesGlobalStudy-wide5008T=0.369C=0.631
1000GenomesSouth AsianSub978T=0.290C=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.216C=0.784
The Genome Aggregation DatabaseAfricanSub8670T=0.662C=0.338
The Genome Aggregation DatabaseAmericanSub834T=0.270C=0.730
The Genome Aggregation DatabaseEast AsianSub1598T=0.262C=0.738
The Genome Aggregation DatabaseEuropeSub18348T=0.226C=0.773
The Genome Aggregation DatabaseGlobalStudy-wide29748T=0.356C=0.643
The Genome Aggregation DatabaseOtherSub298T=0.230C=0.770
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.408C=0.591
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.221C=0.779
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
rs24878911.48E-05alcohol and nictotine co-dependence20158304

eQTL of rs2487891 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 rs2487891 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 )
chr10100842025100842093E06842193
chr10100844646100844696E06844814
chr10100844698100844869E06844866
chr10100845100100845150E06845268
chr10100817723100817951E08117891
chr10100817975100818087E08118143
chr10100818134100818347E08118302
chr10100818511100819009E08118679
chr10100840070100840217E08140238
chr10100840274100840614E08140442
chr10100817517100817672E08217685
chr10100818511100819009E08218679