Variant report

Variant	rs6559750
Chromosome Location	chr9:86538572-86538573
allele	G/T
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	PBX3	chr9:86538517-86538667	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86534503..86538702-chr9:86568820..86574555,7	MCF-7	breast:

Variant related genes	Relation type
KIF27	TF binding region
ENSG00000165118	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10124390	0.87[CHB][hapmap]
rs10868058	0.89[CEU][hapmap];0.91[CHB][hapmap]
rs10868074	0.86[ASN][1000 genomes]
rs10868077	0.82[CHB][hapmap]
rs10868079	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs11140240	0.85[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs11792634	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs12349272	0.92[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs12377335	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12551039	0.83[CHB][hapmap]
rs1572030	0.87[CHB][hapmap]
rs1572031	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs192705	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2065516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2780142	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs295274	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs295275	0.81[EUR][1000 genomes]
rs295291	0.92[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs296885	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs296891	0.87[CHB][hapmap]
rs296892	0.83[CHB][hapmap]
rs3119753	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4297107	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4877815	0.83[CHB][hapmap]
rs6559754	0.87[CHB][hapmap]
rs6559756	0.83[CHB][hapmap]
rs7021189	0.83[CHB][hapmap]
rs7024316	0.86[ASN][1000 genomes]
rs7026436	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754144	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7855503	0.92[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs7865878	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7875011	0.83[CHB][hapmap]
rs7875289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs796001	0.83[CHB][hapmap]
rs9314723	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][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	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv438108	chr9:86488586-86542206	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
7	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86537000-86543800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:86537000-86553600	Weak transcription	Fetal Intestine Small	intestine
4	chr9:86537000-86553600	Weak transcription	Thymus	Thymus
5	chr9:86537200-86545600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:86537800-86542600	Weak transcription	Primary monocytes fromperipheralblood	blood

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