Variant report

Variant	rs62572384
Chromosome Location	chr9:95646489-95646490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95644477..95647026-chr9:95856409..95858869,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGD3-3	chr9:95646467-95646908	NONHSAT133213

Variant related genes	Relation type
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10992511	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10992514	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10992515	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10992528	0.89[EUR][1000 genomes]
rs1323276	0.83[EUR][1000 genomes]
rs41301515	0.82[AFR][1000 genomes]
rs4595187	0.82[EUR][1000 genomes]
rs62572365	0.84[EUR][1000 genomes]
rs62572366	0.81[EUR][1000 genomes]
rs62572367	0.84[EUR][1000 genomes]
rs62572368	0.84[EUR][1000 genomes]
rs62572372	0.84[EUR][1000 genomes]
rs62572374	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62572381	0.83[EUR][1000 genomes]
rs62572386	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62572407	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62572408	0.92[EUR][1000 genomes]
rs62574701	0.83[EUR][1000 genomes]
rs72741010	0.84[EUR][1000 genomes]
rs72741018	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv893574	chr9:95580376-95688099	Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv972781	chr9:95639258-95671744	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
4	nsv982544	chr9:95644425-95647585	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95640600-95648800	Weak transcription	Thymus	Thymus
2	chr9:95640800-95647800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:95640800-95648600	Weak transcription	Primary T cells from cord blood	blood
4	chr9:95640800-95648600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:95641000-95646600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr9:95641000-95648400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr9:95644600-95646800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:95644600-95647200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:95645000-95647000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
10	chr9:95645200-95647000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:95645800-95646800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr9:95645800-95646800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:95645800-95647200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr9:95646000-95646600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr9:95646000-95646600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr9:95646000-95646600	Enhancers	Fetal Muscle Trunk	muscle
17	chr9:95646200-95646600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr9:95646400-95646800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
19	chr9:95646400-95646800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:95646400-95646800	Enhancers	Primary T helper cells fromperipheralblood	blood

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