Variant report

Variant	rs10961003
Chromosome Location	chr9:13279944-13279945
allele	A/G
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	chr9:13279300-13280284	MCF10A-Er-Src	breast:	n/a	n/a
2	CREB1	chr9:13279252-13279948	HepG2	liver:	n/a	n/a
3	BACH1	chr9:13279363-13279954	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F4	chr9:13279469-13280218	MCF10A-Er-Src	breast:	n/a	chr9:13279740-13279749 chr9:13279616-13279625
5	MAX	chr9:13278153-13280005	A549	lung:	n/a	n/a
6	MAZ	chr9:13277767-13280234	IMR90	lung:	n/a	n/a
7	NRF1	chr9:13278989-13280307	SK-N-SH	brain:	n/a	chr9:13279616-13279625 chr9:13279407-13279416 chr9:13279313-13279327
8	NFYB	chr9:13279559-13280082	K562	blood:	n/a	chr9:13279740-13279750
9	TBL1XR1	chr9:13279904-13280164	K562	blood:	n/a	n/a
10	RCOR1	chr9:13279394-13280070	K562	blood:	n/a	n/a
11	MAX	chr9:13278039-13280062	A549	lung:	n/a	n/a
12	HA-E2F1	chr9:13279310-13280078	MCF-7	breast:	n/a	chr9:13279406-13279416 chr9:13279740-13279749 chr9:13279616-13279625
13	MAZ	chr9:13278115-13280073	K562	blood:	n/a	n/a
14	POLR2A	chr9:13277998-13279975	IMR90	lung:	n/a	n/a
15	ZNF384	chr9:13279713-13280029	K562	blood:	n/a	n/a
16	POLR2A	chr9:13279037-13280410	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:55977919..55980808-chr9:13278471..13279995,2	MCF-7	breast:
2	chr9:13278089..13282078-chr9:14313109..14316114,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234740	TF binding region
MPDZ	TF binding region
ENSG00000147862	Chromatin interaction
ENSG00000180891	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10756466	0.86[ASN][1000 genomes]
rs10960994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10960995	0.89[ASN][1000 genomes]
rs10960996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10960997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10960998	0.89[ASN][1000 genomes]
rs10960999	0.99[ASN][1000 genomes]
rs10961004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10961005	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10961007	0.92[ASN][1000 genomes]
rs10961009	0.91[ASN][1000 genomes]
rs1330136	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73647125	0.93[ASN][1000 genomes]
rs7847055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7855845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9696523	1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv892583	chr9:13166139-13350478	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv892584	chr9:13214871-13350478	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv427838	chr9:13229753-13393890	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3376897	chr9:13277977-13280925	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
6	esv3405883	chr9:13278702-13280900	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13277800-13280000	Active TSS	Brain Anterior Caudate	brain
2	chr9:13277800-13280000	Active TSS	Colon Smooth Muscle	Colon
3	chr9:13277800-13280000	Active TSS	Fetal Brain Female	brain
4	chr9:13277800-13280000	Active TSS	A549	lung
5	chr9:13277800-13280000	Active TSS	Osteobl	bone
6	chr9:13277800-13280200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:13277800-13280200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr9:13277800-13280200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:13277800-13280200	Active TSS	Aorta	Aorta
10	chr9:13277800-13280200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr9:13277800-13280200	Active TSS	NHLF	lung
12	chr9:13277800-13280400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr9:13277800-13280400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr9:13278000-13280000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:13278000-13280000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:13278000-13280000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:13278000-13280000	Active TSS	Brain Angular Gyrus	brain
18	chr9:13278000-13280000	Active TSS	Brain Germinal Matrix	brain
19	chr9:13278000-13280000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:13278000-13280000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr9:13278000-13280000	Active TSS	Fetal Kidney	kidney
22	chr9:13278000-13280000	Active TSS	HSMM	muscle
23	chr9:13278000-13280000	Active TSS	K562	blood
24	chr9:13278000-13280000	Active TSS	NHDF-Ad	bronchial
25	chr9:13278000-13280200	Active TSS	H1 Cell Line	embryonic stem cell
26	chr9:13278000-13280200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:13278000-13280200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:13278000-13280200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:13278000-13280200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr9:13278000-13280200	Active TSS	Right Atrium	heart
31	chr9:13278000-13280200	Active TSS	Right Ventricle	heart
32	chr9:13278000-13280200	Active TSS	HSMMtube	muscle
33	chr9:13278000-13280400	Active TSS	Brain Cingulate Gyrus	brain
34	chr9:13278000-13280400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr9:13278200-13280000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:13278200-13280000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:13278200-13280000	Active TSS	Fetal Lung	lung
38	chr9:13278200-13280000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr9:13278200-13280000	Active TSS	HepG2	liver
40	chr9:13278200-13280200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr9:13278200-13280200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:13278200-13280200	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr9:13278200-13280200	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr9:13278200-13280200	Active TSS	Brain Substantia Nigra	brain
45	chr9:13278200-13280200	Active TSS	Left Ventricle	heart
46	chr9:13278200-13280200	Active TSS	Psoas Muscle	Psoas
47	chr9:13278200-13280200	Active TSS	Rectal Smooth Muscle	rectum
48	chr9:13278200-13280400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:13278200-13280400	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr9:13278400-13280000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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