Variant report

Variant	rs11140308
Chromosome Location	chr9:86569176-86569177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86566551..86568592-chr9:86569030..86570936,2	K562	blood:
2	chr9:86548960..86550790-chr9:86568981..86570981,2	MCF-7	breast:
3	chr9:86534503..86538702-chr9:86568820..86574555,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10780645	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs10868067	0.93[EUR][1000 genomes]
rs11140238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11140252	1.00[CHB][hapmap]
rs11140254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.82[ASN][1000 genomes]
rs11140280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs11140288	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11140290	0.86[EUR][1000 genomes]
rs11140291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11140292	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11140294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11140296	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11140302	0.91[ASN][1000 genomes]
rs11140309	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140310	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]
rs11140312	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140313	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140316	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]
rs11140318	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140321	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11140322	1.00[EUR][1000 genomes];0.86[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];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12056961	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12235653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12235969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12237056	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12237297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2017558	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3750407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59409125	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60989495	0.86[EUR][1000 genomes]
rs73471357	1.00[EUR][1000 genomes];0.86[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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86543000-86571000	Weak transcription	Esophagus	oesophagus
3	chr9:86547200-86570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:86549000-86570200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr9:86550200-86570400	Weak transcription	Aorta	Aorta
6	chr9:86550400-86569200	Weak transcription	Fetal Heart	heart
7	chr9:86550400-86570400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:86550800-86570400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:86551000-86570400	Weak transcription	Stomach Mucosa	stomach
10	chr9:86551000-86570400	Weak transcription	NH-A	brain
11	chr9:86551600-86570000	Weak transcription	Fetal Brain Male	brain
12	chr9:86551600-86570200	Weak transcription	NHEK	skin
13	chr9:86552000-86570400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:86552000-86570400	Weak transcription	Spleen	Spleen
15	chr9:86553000-86570400	Weak transcription	Colonic Mucosa	Colon
16	chr9:86553600-86570000	Strong transcription	Fetal Stomach	stomach
17	chr9:86553800-86569800	Weak transcription	Hela-S3	cervix
18	chr9:86554400-86570400	Weak transcription	Psoas Muscle	Psoas
19	chr9:86554600-86570200	Weak transcription	Brain Substantia Nigra	brain
20	chr9:86554800-86570400	Weak transcription	Pancreas	Pancrea
21	chr9:86554800-86570600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:86555400-86570200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr9:86555600-86570200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr9:86556000-86570200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:86556000-86571000	Weak transcription	Gastric	stomach
26	chr9:86556200-86570400	Weak transcription	HSMMtube	muscle
27	chr9:86557000-86571000	Weak transcription	Lung	lung
28	chr9:86557400-86570000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr9:86557400-86570400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr9:86557600-86570200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:86557800-86570400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr9:86557800-86570400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:86558000-86570000	Weak transcription	Dnd41	blood
34	chr9:86558000-86570200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:86558000-86570200	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:86558000-86570400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:86558000-86571000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr9:86558400-86570200	Weak transcription	Primary T cells from cord blood	blood
39	chr9:86558600-86570200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr9:86558600-86570200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr9:86558600-86570400	Weak transcription	Brain Angular Gyrus	brain
42	chr9:86559200-86570000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:86559400-86570200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr9:86559400-86570200	Weak transcription	Fetal Brain Female	brain
45	chr9:86559800-86570200	Weak transcription	Primary B cells from cord blood	blood
46	chr9:86559800-86570200	Weak transcription	NHDF-Ad	bronchial
47	chr9:86560000-86570000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr9:86560000-86570200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr9:86560000-86570200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr9:86560000-86570200	Weak transcription	A549	lung

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