Variant report

Variant	rs2296060
Chromosome Location	chr9:95645020-95645021
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:95644760-95645021	H1-hESC	embryonic stem cell:	n/a	n/a

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	chr9:95644865-95645071	NONHSAT133210
2	lnc-FGD3-3	chr9:95644849-95645071	NONHSAT133209

Variant related genes	Relation type
ZNF484	TF binding region
ENSG00000226668	TF binding region
ENSG00000223446	Chromatin interaction
ENSG00000165233	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10115872	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs10123843	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1022833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs10739933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10739934	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10821030	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10821035	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10992489	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12003440	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs12336022	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12337654	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13293147	0.88[JPT][hapmap]
rs13294147	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4078292	0.86[JPT][hapmap]
rs4744150	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4744151	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6479434	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7032277	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7035881	0.86[JPT][hapmap]
rs7039812	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7040645	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7043469	0.88[JPT][hapmap]

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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95640600-95645800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr9:95640600-95648800	Weak transcription	Thymus	Thymus
3	chr9:95640800-95645200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:95640800-95646000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:95640800-95646400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:95640800-95647800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:95640800-95648600	Weak transcription	Primary T cells from cord blood	blood
8	chr9:95640800-95648600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:95641000-95646000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:95641000-95646600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr9:95641000-95648400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr9:95644400-95645400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr9:95644400-95645400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr9:95644600-95646000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr9:95644600-95646800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr9:95644600-95647200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:95644800-95645600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr9:95644800-95646400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:95645000-95645200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr9:95645000-95645400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr9:95645000-95646400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr9:95645000-95646400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:95645000-95647000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

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