Variant report

Variant	rs10479560
Chromosome Location	chr5:179508424-179508425
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179505750..179508557-chr5:179532943..179534980,2	MCF-7	breast:
2	chr5:179497673..179499506-chr5:179506903..179509868,3	MCF-7	breast:
3	chr5:179499305..179501402-chr5:179506576..179508838,2	K562	blood:
4	chr5:179503309..179506664-chr5:179506788..179509902,3	K562	blood:
5	chr5:179505842..179508438-chr5:179517931..179520878,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF130-3	chr5:179505357-179508661	NONHSAT105668

No data

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10067073	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10072792	0.84[EUR][1000 genomes]
rs10078845	1.00[CEU][hapmap]
rs10479556	1.00[CEU][hapmap]
rs10479558	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10479559	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10516141	1.00[CEU][hapmap]
rs1110145	0.92[EUR][1000 genomes]
rs11952090	0.92[EUR][1000 genomes]
rs12514260	1.00[CEU][hapmap]
rs12516233	1.00[CEU][hapmap]
rs12516364	1.00[CEU][hapmap]
rs12516629	1.00[CEU][hapmap]
rs12516767	1.00[CEU][hapmap]
rs12521819	0.84[EUR][1000 genomes]
rs13354862	1.00[CEU][hapmap]
rs13362131	1.00[CEU][hapmap]
rs1345085	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1345087	0.96[EUR][1000 genomes]
rs1345088	0.96[EUR][1000 genomes]
rs17079941	1.00[CEU][hapmap]
rs1808088	1.00[CEU][hapmap]
rs28478989	0.84[EUR][1000 genomes]
rs4623110	1.00[CEU][hapmap]
rs59668758	0.84[EUR][1000 genomes]
rs9654545	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179499400-179517000	Weak transcription	Right Atrium	heart
2	chr5:179505600-179509600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:179507200-179509200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:179507400-179509200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:179507600-179508600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr5:179507600-179508800	Bivalent Enhancer	Fetal Thymus	thymus
7	chr5:179507800-179511200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:179508000-179509400	Enhancers	Liver	Liver
9	chr5:179508000-179513000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:179508200-179511200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:179508400-179508800	Flanking Active TSS	HepG2	liver
12	chr5:179508400-179510000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:179508400-179511200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:179508400-179511600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:179508400-179513000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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