Variant report

Variant	rs11140310
Chromosome Location	chr9:86572525-86572526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:86570432-86572584	K562	blood:	n/a	n/a
2	POLR2A	chr9:86572518-86573336	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:86570881-86572525	GM12891	blood:	n/a	n/a
4	POLR2A	chr9:86570844-86572528	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:86534561..86538164-chr9:86570673..86573880,3	K562	blood:
2	chr9:86321564..86323208-chr9:86572109..86574436,2	MCF-7	breast:
3	chr9:86237033..86239481-chr9:86571525..86573399,2	MCF-7	breast:
4	chr9:86534003..86537844-chr9:86570557..86574103,8	K562	blood:
5	chr9:86534503..86538702-chr9:86568820..86574555,7	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf64	TF binding region
ENSG00000148057	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10780645	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10868067	0.93[EUR][1000 genomes]
rs11140238	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11140252	1.00[CHB][hapmap]
rs11140254	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11140269	0.85[EUR][1000 genomes]
rs11140270	0.85[EUR][1000 genomes]
rs11140271	1.00[EUR][1000 genomes]
rs11140274	0.92[EUR][1000 genomes]
rs11140275	0.92[EUR][1000 genomes]
rs11140280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11140288	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11140290	0.86[EUR][1000 genomes]
rs11140291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11140292	1.00[EUR][1000 genomes]
rs11140294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[EUR][1000 genomes]
rs11140296	1.00[EUR][1000 genomes]
rs11140308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140309	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140312	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140313	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140318	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140321	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140322	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140337	1.00[EUR][1000 genomes]
rs11140338	1.00[EUR][1000 genomes]
rs11140355	1.00[GIH][hapmap]
rs11531847	1.00[EUR][1000 genomes]
rs11533022	1.00[EUR][1000 genomes]
rs11533047	0.93[EUR][1000 genomes]
rs11535577	1.00[EUR][1000 genomes]
rs11559387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs12056961	1.00[EUR][1000 genomes]
rs12235653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12235969	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12237056	1.00[EUR][1000 genomes]
rs12237297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017558	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59409125	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60989495	0.86[EUR][1000 genomes]
rs73471357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9776332	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
7	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86570400-86572600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:86570400-86572600	Active TSS	HSMMtube	muscle
3	chr9:86570600-86572600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:86570800-86572600	Active TSS	Colonic Mucosa	Colon
5	chr9:86571000-86572600	Active TSS	Brain Angular Gyrus	brain
6	chr9:86571000-86572600	Active TSS	Brain Substantia Nigra	brain
7	chr9:86571000-86572600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr9:86571000-86572600	Active TSS	Fetal Kidney	kidney
9	chr9:86571000-86572600	Active TSS	Stomach Mucosa	stomach
10	chr9:86571200-86572600	Active TSS	Fetal Intestine Large	intestine
11	chr9:86571200-86572600	Active TSS	Small Intestine	intestine
12	chr9:86571400-86572600	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr9:86571600-86572600	Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr9:86571800-86572600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:86571800-86584600	Weak transcription	Spleen	Spleen
16	chr9:86572000-86572600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr9:86572000-86572600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:86572000-86572600	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr9:86572000-86572600	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr9:86572000-86572600	Flanking Active TSS	A549	lung
21	chr9:86572000-86572600	Flanking Active TSS	Dnd41	blood
22	chr9:86572000-86572600	Flanking Active TSS	HepG2	liver
23	chr9:86572000-86572600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr9:86572000-86577200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:86572000-86586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:86572200-86572600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr9:86572200-86572600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr9:86572200-86572600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:86572200-86572600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr9:86572200-86572600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:86572200-86572600	Flanking Active TSS	Liver	Liver
32	chr9:86572200-86572600	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr9:86572200-86572600	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr9:86572200-86572600	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr9:86572200-86572600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr9:86572200-86572600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr9:86572200-86572600	Flanking Active TSS	Rectal Smooth Muscle	rectum
38	chr9:86572200-86572600	Flanking Active TSS	K562	blood
39	chr9:86572200-86572600	Flanking Active TSS	NHDF-Ad	bronchial
40	chr9:86572200-86573600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:86572200-86576000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:86572200-86577000	Weak transcription	HMEC	breast
43	chr9:86572200-86577200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:86572200-86579800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:86572200-86581000	Weak transcription	Primary T cells from cord blood	blood
46	chr9:86572200-86581000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr9:86572200-86581200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:86572200-86581600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr9:86572200-86581800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr9:86572200-86581800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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