Variant report

Variant	rs11140316
Chromosome Location	chr9:86593443-86593444
allele	C/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	POLR2A	chr9:86593110-86595750	A549	lung:	n/a	n/a
2	POLR2A	chr9:86593061-86596929	SK-N-MC	brain:	n/a	n/a
3	CCNT2	chr9:86593336-86593622	K562	blood:	n/a	n/a
4	POLR2A	chr9:86593227-86593480	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:86592005-86597005	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
7	POLR2A	chr9:86589056-86597036	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:86593242-86595931	U87	brain:	n/a	n/a
9	MYC	chr9:86593418-86593736	MCF10A-Er-Src	breast:	n/a	n/a
10	NFATC1	chr9:86592763-86594905	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:86593185-86597118	GM12878	blood:	n/a	n/a
12	SIN3A	chr9:86592976-86596804	H1-hESC	embryonic stem cell:	n/a	n/a
13	NFATC1	chr9:86592990-86596378	GM12878	blood:	n/a	n/a
14	POLR2A	chr9:86593233-86595960	HCT-116	colon:	n/a	n/a
15	POLR2A	chr9:86593285-86595900	HepG2	liver:	n/a	n/a
16	POLR2A	chr9:86593273-86593561	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr9:86593306-86596828	HepG2	liver:	n/a	n/a
18	POLR2A	chr9:86593206-86593456	MCF-7	breast:	n/a	n/a
19	POLR2A	chr9:86592943-86593449	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr9:86593200-86596145	U87	brain:	n/a	n/a
21	POLR2A	chr9:86593339-86596844	Hela-S3	cervix:	n/a	n/a
22	CHD1	chr9:86593158-86596789	IMR90	lung:	n/a	chr9:86595578-86595587 chr9:86596056-86596066 chr9:86595550-86595560 chr9:86595273-86595283
23	TBL1XR1	chr9:86593395-86595834	K562	blood:	n/a	n/a
24	POLR2A	chr9:86593190-86596233	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr9:86593206-86596139	U87	brain:	n/a	n/a
26	POLR2A	chr9:86593425-86593691	SK-N-SH	brain:	n/a	n/a
27	SP1	chr9:86592919-86593574	H1-hESC	embryonic stem cell:	n/a	n/a
28	WRNIP1	chr9:86593322-86593485	GM12878	blood:	n/a	n/a
29	REST	chr9:86593207-86597147	H1-neurons	neurons:	n/a	chr9:86595761-86595774 chr9:86596021-86596039 chr9:86594642-86594655
30	POLR2A	chr9:86593163-86597264	GM12891	blood:	n/a	n/a
31	CHD1	chr9:86592725-86596929	H1-hESC	embryonic stem cell:	n/a	chr9:86595578-86595587 chr9:86596056-86596066 chr9:86595550-86595560 chr9:86595273-86595283
32	POLR2A	chr9:86593040-86596859	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62432743..62434322-chr9:86593092..86595353,2	MCF-7	breast:
2	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
3	chr9:86593378..86594996-chr9:86858039..86859653,2	MCF-7	breast:
4	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
5	chr17:57914983..57917065-chr9:86592190..86594994,2	MCF-7	breast:
6	chr9:86534520..86537940-chr9:86592614..86595774,6	K562	blood:
7	chr9:86593375..86596264-chr9:101558546..101560057,2	MCF-7	breast:
8	chr9:86592736..86597542-chr9:86606160..86610925,6	K562	blood:
9	chr9:86533247..86537973-chr9:86593370..86597981,20	MCF-7	breast:

Variant related genes	Relation type
RMI1	TF binding region
HNRNPK	TF binding region
ENSG00000202523	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000165138	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10780645	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10868067	0.93[EUR][1000 genomes]
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]
rs11140310	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]
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]
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[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];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]
rs4480186	0.85[MKK][hapmap]
rs59409125	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60989495	0.86[EUR][1000 genomes]
rs73469392	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73471357	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs969148	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9776332	0.93[EUR][1000 genomes]

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	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
2	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
3	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
4	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
5	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
6	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
7	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86590000-86594400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr9:86590600-86593800	Weak transcription	Gastric	stomach
3	chr9:86590600-86594000	Weak transcription	Spleen	Spleen
4	chr9:86590800-86593800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:86590800-86594400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:86591000-86594400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
7	chr9:86591200-86594400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
8	chr9:86591400-86594400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:86591400-86594600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
10	chr9:86591600-86593600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
11	chr9:86591600-86596600	Active TSS	Ovary	ovary
12	chr9:86591800-86593600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr9:86591800-86597000	Active TSS	Psoas Muscle	Psoas
14	chr9:86592000-86594200	Transcr. at gene 5' and 3'	K562	blood
15	chr9:86592200-86593600	Transcr. at gene 5' and 3'	NHEK	skin
16	chr9:86592200-86594400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:86592200-86594400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
18	chr9:86592200-86594400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
19	chr9:86592200-86594400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
20	chr9:86592200-86594400	Transcr. at gene 5' and 3'	A549	lung
21	chr9:86592200-86594600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:86592200-86596800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:86592200-86597000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:86592400-86593600	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr9:86592400-86594200	Transcr. at gene 5' and 3'	Osteobl	bone
26	chr9:86592400-86596200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:86592400-86596400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr9:86592400-86596600	Active TSS	Aorta	Aorta
29	chr9:86592400-86596800	Active TSS	Right Ventricle	heart
30	chr9:86592400-86597600	Active TSS	Fetal Brain Female	brain
31	chr9:86592600-86596200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:86592600-86596400	Active TSS	HSMMtube	muscle
33	chr9:86592600-86596600	Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr9:86592600-86596600	Active TSS	Thymus	Thymus
35	chr9:86592600-86596800	Active TSS	Right Atrium	heart
36	chr9:86592600-86597000	Active TSS	Stomach Smooth Muscle	stomach
37	chr9:86592800-86594000	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr9:86592800-86594000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:86592800-86595000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
40	chr9:86592800-86595400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:86592800-86596400	Active TSS	Fetal Muscle Leg	muscle
42	chr9:86592800-86596400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr9:86592800-86596400	Active TSS	HMEC	breast
44	chr9:86592800-86596600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr9:86592800-86596600	Active TSS	Fetal Intestine Large	intestine
46	chr9:86592800-86596600	Active TSS	Fetal Intestine Small	intestine
47	chr9:86592800-86596800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:86592800-86597200	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr9:86592800-86597200	Active TSS	NHLF	lung
50	chr9:86593000-86593600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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