Variant report

Variant	rs1809660
Chromosome Location	chr5:57246446-57246447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10037252	0.89[EUR][1000 genomes]
rs10053148	0.89[EUR][1000 genomes]
rs10054634	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10068767	0.87[EUR][1000 genomes]
rs10080109	0.89[EUR][1000 genomes]
rs1026371	0.82[AMR][1000 genomes]
rs1027163	1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1037559	0.89[EUR][1000 genomes]
rs10940586	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11743935	0.89[EUR][1000 genomes]
rs1304354	0.89[EUR][1000 genomes]
rs13173455	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs13186838	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs1349955	0.88[EUR][1000 genomes]
rs1349956	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1378246	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378247	0.89[EUR][1000 genomes]
rs1387634	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1454907	0.95[ASN][1000 genomes]
rs1454916	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1454919	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1454922	0.89[EUR][1000 genomes]
rs1454923	0.87[EUR][1000 genomes]
rs1454927	0.82[AMR][1000 genomes]
rs1489785	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1489787	0.89[EUR][1000 genomes]
rs1489788	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1489789	0.89[EUR][1000 genomes]
rs1489796	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1546035	0.89[EUR][1000 genomes]
rs1565339	0.89[EUR][1000 genomes]
rs1602155	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1826098	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1826099	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1840394	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1844436	0.89[EUR][1000 genomes]
rs1948276	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015208	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2198636	0.83[EUR][1000 genomes]
rs35603705	0.84[AMR][1000 genomes]
rs4429810	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4699919	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6450448	0.82[AMR][1000 genomes]
rs6450454	0.89[EUR][1000 genomes]
rs6450455	0.89[EUR][1000 genomes]
rs6450456	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6450457	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6864437	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6879399	0.86[AMR][1000 genomes]
rs7710627	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7714449	0.89[EUR][1000 genomes]
rs7715831	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs7722307	0.89[EUR][1000 genomes]
rs7725138	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9292147	0.89[EUR][1000 genomes]
rs9292149	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9292150	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs971399	0.85[EUR][1000 genomes]
rs995442	0.89[EUR][1000 genomes]
rs995443	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1792273	chr5:57214817-57320343	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1028794	chr5:57242812-57256096	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1809660	HSPB3	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57243400-57247200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:57246200-57246800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:57246400-57246800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:57246400-57246800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr5:57246400-57246800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:57246400-57247000	Enhancers	H9 Cell Line	embryonic stem cell
7	chr5:57246400-57247000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:57246400-57247000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr5:57246400-57247000	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links