Variant report

Variant	rs139926461
Chromosome Location	chr9:13279646-13279647
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	E2F6	chr9:13279341-13279848	K562	blood:	n/a	chr9:13279406-13279416 chr9:13279740-13279749 chr9:13279616-13279625
2	POLR2A	chr9:13279243-13279804	K562	blood:	n/a	n/a
3	POLR2A	chr9:13279280-13279845	K562	blood:	n/a	n/a
4	POLR2A	chr9:13278255-13279891	A549	lung:	n/a	n/a
5	MAX	chr9:13279364-13279821	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:13279278-13279858	A549	lung:	n/a	n/a
7	POLR2A	chr9:13278266-13279831	K562	blood:	n/a	n/a
8	MAX	chr9:13279307-13279885	ECC-1	luminal epithelium:	n/a	n/a
9	NFYA	chr9:13279638-13279819	Hela-S3	cervix:	n/a	chr9:13279738-13279756 chr9:13279740-13279750
10	YY1	chr9:13279298-13279813	HepG2	liver:	n/a	chr9:13279657-13279668 chr9:13279695-13279706 chr9:13279689-13279703
11	POLR2A	chr9:13279300-13280284	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr9:13279305-13279845	MCF-7	breast:	n/a	n/a
13	POLR2A	chr9:13279273-13279720	SK-N-SH	brain:	n/a	n/a
14	TBP	chr9:13279402-13279825	K562	blood:	n/a	n/a
15	POLR2A	chr9:13278002-13279756	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr9:13279600-13279750	AG04449	skin:	n/a	n/a
17	POLR2A	chr9:13279268-13279798	A549	lung:	n/a	n/a
18	MAX	chr9:13279387-13279755	HepG2	liver:	n/a	n/a
19	POLR2A	chr9:13279270-13279810	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr9:13279282-13279680	SK-N-SH	brain:	n/a	n/a
21	CREB1	chr9:13279252-13279948	HepG2	liver:	n/a	n/a
22	TCF12	chr9:13279336-13279835	ECC-1	luminal epithelium:	n/a	n/a
23	CHD2	chr9:13279436-13279848	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr9:13279264-13279868	HepG2	liver:	n/a	n/a
25	POLR2A	chr9:13279349-13279844	SK-N-MC	brain:	n/a	n/a
26	BACH1	chr9:13279363-13279954	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr9:13279537-13279761	SK-N-SH_RA	brain:	n/a	n/a
28	ZBTB7A	chr9:13279309-13279792	ECC-1	luminal epithelium:	n/a	chr9:13279617-13279626
29	POLR2A	chr9:13279269-13279767	H1-hESC	embryonic stem cell:	n/a	n/a
30	TEAD4	chr9:13279552-13279834	H1-hESC	embryonic stem cell:	n/a	n/a
31	E2F6	chr9:13279296-13279761	K562	blood:	n/a	chr9:13279406-13279416 chr9:13279740-13279749 chr9:13279616-13279625
32	POLR2A	chr9:13278133-13279750	HepG2	liver:	n/a	n/a
33	HDAC2	chr9:13279284-13279802	HepG2	liver:	n/a	n/a
34	POLR2A	chr9:13279244-13279828	K562	blood:	n/a	n/a
35	CHD2	chr9:13279406-13279700	HepG2	liver:	n/a	n/a
36	E2F4	chr9:13279469-13280218	MCF10A-Er-Src	breast:	n/a	chr9:13279740-13279749 chr9:13279616-13279625
37	HEY1	chr9:13279310-13279677	K562	blood:	n/a	chr9:13279657-13279672 chr9:13279406-13279421 chr9:13279610-13279625 chr9:13279637-13279652
38	ELF1	chr9:13279510-13279776	K562	blood:	n/a	chr9:13279672-13279684 chr9:13279665-13279674
39	EGR1	chr9:13279244-13279855	K562	blood:	n/a	chr9:13279485-13279498 chr9:13279618-13279628 chr9:13279485-13279498 chr9:13279429-13279442 chr9:13279314-13279323 chr9:13279486-13279496 chr9:13279484-13279498 chr9:13279429-13279442 chr9:13279674-13279684 chr9:13279486-13279495 chr9:13279486-13279496 chr9:13279428-13279443 chr9:13279485-13279498 chr9:13279617-13279630
40	BHLHE40	chr9:13279384-13279648	K562	blood:	n/a	n/a
41	HEY1	chr9:13279241-13279805	HepG2	liver:	n/a	chr9:13279657-13279672 chr9:13279406-13279421 chr9:13279610-13279625 chr9:13279637-13279652
42	EGR1	chr9:13279238-13279771	K562	blood:	n/a	chr9:13279485-13279498 chr9:13279618-13279628 chr9:13279485-13279498 chr9:13279429-13279442 chr9:13279314-13279323 chr9:13279486-13279496 chr9:13279484-13279498 chr9:13279429-13279442 chr9:13279674-13279684 chr9:13279486-13279495 chr9:13279486-13279496 chr9:13279428-13279443 chr9:13279485-13279498 chr9:13279617-13279630
43	SIN3A	chr9:13279419-13279861	H1-hESC	embryonic stem cell:	n/a	chr9:13279608-13279619
44	POLR2A	chr9:13279283-13279851	ECC-1	luminal epithelium:	n/a	n/a
45	MAX	chr9:13278153-13280005	A549	lung:	n/a	n/a
46	POLR2A	chr9:13277875-13279931	HUVEC	blood vessel:	n/a	n/a
47	MAZ	chr9:13277767-13280234	IMR90	lung:	n/a	n/a
48	NRF1	chr9:13278989-13280307	SK-N-SH	brain:	n/a	chr9:13279616-13279625 chr9:13279407-13279416 chr9:13279313-13279327
49	NFIC	chr9:13279300-13279856	ECC-1	luminal epithelium:	n/a	n/a
50	MAX	chr9:13279306-13279843	K562	blood:	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
MPDZ	TF binding region
ENSG00000234740	TF binding region
ENSG00000147862	Chromatin interaction
ENSG00000180891	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13277600-13279800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:13277800-13280000	Active TSS	Brain Anterior Caudate	brain
3	chr9:13277800-13280000	Active TSS	Colon Smooth Muscle	Colon
4	chr9:13277800-13280000	Active TSS	Fetal Brain Female	brain
5	chr9:13277800-13280000	Active TSS	A549	lung
6	chr9:13277800-13280000	Active TSS	Osteobl	bone
7	chr9:13277800-13280200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr9:13277800-13280200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr9:13277800-13280200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:13277800-13280200	Active TSS	Aorta	Aorta
11	chr9:13277800-13280200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr9:13277800-13280200	Active TSS	NHLF	lung
13	chr9:13277800-13280400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr9:13277800-13280400	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr9:13278000-13279800	Active TSS	Primary hematopoietic stem cells	blood
16	chr9:13278000-13280000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:13278000-13280000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:13278000-13280000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:13278000-13280000	Active TSS	Brain Angular Gyrus	brain
20	chr9:13278000-13280000	Active TSS	Brain Germinal Matrix	brain
21	chr9:13278000-13280000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:13278000-13280000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
23	chr9:13278000-13280000	Active TSS	Fetal Kidney	kidney
24	chr9:13278000-13280000	Active TSS	HSMM	muscle
25	chr9:13278000-13280000	Active TSS	K562	blood
26	chr9:13278000-13280000	Active TSS	NHDF-Ad	bronchial
27	chr9:13278000-13280200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr9:13278000-13280200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:13278000-13280200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:13278000-13280200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr9:13278000-13280200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr9:13278000-13280200	Active TSS	Right Atrium	heart
33	chr9:13278000-13280200	Active TSS	Right Ventricle	heart
34	chr9:13278000-13280200	Active TSS	HSMMtube	muscle
35	chr9:13278000-13280400	Active TSS	Brain Cingulate Gyrus	brain
36	chr9:13278000-13280400	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr9:13278200-13279800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:13278200-13279800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:13278200-13279800	Active TSS	Esophagus	oesophagus
40	chr9:13278200-13279800	Active TSS	Gastric	stomach
41	chr9:13278200-13279800	Bivalent/Poised TSS	Thymus	Thymus
42	chr9:13278200-13280000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:13278200-13280000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:13278200-13280000	Active TSS	Fetal Lung	lung
45	chr9:13278200-13280000	Active TSS	Placenta Amnion	Placenta Amnion
46	chr9:13278200-13280000	Active TSS	HepG2	liver
47	chr9:13278200-13280200	Active TSS	H9 Cell Line	embryonic stem cell
48	chr9:13278200-13280200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:13278200-13280200	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr9:13278200-13280200	Active TSS	HUES64 Cell Line	embryonic stem cell

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