Variant report

Variant	rs1378247
Chromosome Location	chr5:57285671-57285672
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10037252	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10053148	1.00[EUR][1000 genomes]
rs10054634	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10068767	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10080109	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1027163	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1037559	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940586	0.95[EUR][1000 genomes]
rs11743935	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1304354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13186838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349955	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349956	1.00[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes]
rs1378246	0.92[EUR][1000 genomes]
rs1387633	1.00[ASN][1000 genomes]
rs1387634	0.95[EUR][1000 genomes]
rs1387636	1.00[ASN][1000 genomes]
rs1387637	1.00[ASN][1000 genomes]
rs1454916	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1454919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1454922	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1454923	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489785	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1489787	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489788	0.96[EUR][1000 genomes]
rs1489789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489792	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1489796	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1546035	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1565339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1602155	0.96[EUR][1000 genomes]
rs1809660	0.89[EUR][1000 genomes]
rs1826098	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1826099	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1840394	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1844436	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1948276	0.85[EUR][1000 genomes]
rs1964507	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2015208	0.96[EUR][1000 genomes]
rs2124148	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2198636	0.93[EUR][1000 genomes]
rs4429810	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4699919	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6450454	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6450455	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450456	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs6450457	0.95[EUR][1000 genomes]
rs6864437	0.96[EUR][1000 genomes]
rs6892626	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs724114	0.85[ASN][1000 genomes]
rs72753316	1.00[ASN][1000 genomes]
rs72753324	0.85[ASN][1000 genomes]
rs7710627	0.96[EUR][1000 genomes]
rs7714449	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7715831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722307	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7725138	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9292147	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9292149	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9292150	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9292151	0.91[ASN][1000 genomes]
rs971399	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs995442	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs995443	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv10700	chr5:57277483-57313710	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv1817904	chr5:57277522-57359476	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1829717	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1830976	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1837615	chr5:57277522-57359476	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1846984	chr5:57277522-57359476	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1850205	chr5:57277522-57359476	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1378247	HSPB3	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57284600-57286200	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr5:57284600-57286200	Enhancers	NHEK	skin
3	chr5:57284800-57285800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:57284800-57285800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr5:57284800-57285800	Enhancers	Stomach Mucosa	stomach
6	chr5:57284800-57285800	Enhancers	HMEC	breast
7	chr5:57285000-57285800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:57285000-57285800	Flanking Active TSS	A549	lung
9	chr5:57285000-57285800	Enhancers	HUVEC	blood vessel
10	chr5:57285200-57286000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:57285200-57289200	Weak transcription	Left Ventricle	heart
12	chr5:57285200-57297600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:57285400-57286000	Enhancers	HUES64 Cell Line	embryonic stem cell

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