Variant report

Variant	rs558158260
Chromosome Location	chr11:66885959-66885960
allele	G/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	TCF3	chr11:66885670-66886759	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:66885655-66886224	GM12892	blood:	n/a	n/a
3	TCF12	chr11:66885913-66886309	A549	lung:	n/a	chr11:66886298-66886305
4	MXI1	chr11:66885763-66886097	GM12878	blood:	n/a	n/a
5	YY1	chr11:66885865-66886136	A549	lung:	n/a	chr11:66886062-66886076
6	POLR2A	chr11:66885108-66886634	GM12892	blood:	n/a	n/a
7	POLR2A	chr11:66885710-66885967	GM12891	blood:	n/a	n/a
8	YY1	chr11:66885807-66886211	ECC-1	luminal epithelium:	n/a	chr11:66886062-66886076
9	POLR2A	chr11:66885668-66886127	PBDE	blood:	n/a	n/a
10	POLR2A	chr11:66885780-66886213	A549	lung:	n/a	n/a
11	MAZ	chr11:66885004-66887904	IMR90	lung:	n/a	chr11:66886120-66886129 chr11:66886002-66886011 chr11:66887263-66887273
12	POLR2A	chr11:66884978-66886367	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr11:66885658-66886256	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:66885239-66886986	GM18526	blood:	n/a	n/a
15	TAF7	chr11:66885684-66886254	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr11:66885381-66886231	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr11:66885650-66886252	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr11:66885535-66887011	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:66885924-66886058	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:66885236-66887001	GM12892	blood:	n/a	n/a
21	POU2F2	chr11:66885564-66886073	GM12878	blood:	n/a	n/a
22	ZBTB7A	chr11:66885950-66887409	K562	blood:	n/a	chr11:66887292-66887301 chr11:66887025-66887033 chr11:66886008-66886015
23	POLR2A	chr11:66885165-66887278	GM18505	blood:	n/a	n/a
24	EBF1	chr11:66885785-66886223	GM12878	blood:	n/a	chr11:66885785-66885794 chr11:66885785-66885794
25	ZBTB7A	chr11:66885551-66885960	ECC-1	luminal epithelium:	n/a	n/a
26	MYC	chr11:66885953-66886062	MCF-7	breast:	n/a	chr11:66886002-66886011
27	MAZ	chr11:66885269-66887072	GM12878	blood:	n/a	chr11:66886120-66886129 chr11:66886002-66886011
28	JUND	chr11:66885888-66886199	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr11:66885656-66886818	H1-hESC	embryonic stem cell:	n/a	chr11:66886120-66886129 chr11:66886002-66886011
30	SIN3A	chr11:66885690-66887976	H1-hESC	embryonic stem cell:	n/a	chr11:66886856-66886867 chr11:66886721-66886729
31	TCF7L2	chr11:66885907-66886130	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr11:66885658-66886247	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr11:66885563-66886939	HEK293	kidney:	n/a	n/a
34	MAX	chr11:66885749-66886169	GM12878	blood:	n/a	chr11:66886120-66886129 chr11:66886002-66886011
35	POLR2A	chr11:66885668-66886095	HUVEC	blood vessel:	n/a	n/a
36	YY1	chr11:66885721-66886192	H1-hESC	embryonic stem cell:	n/a	chr11:66886062-66886076
37	YY1	chr11:66885605-66886139	GM12891	blood:	n/a	chr11:66886062-66886076
38	GABPA	chr11:66885781-66886126	H1-hESC	embryonic stem cell:	n/a	n/a
39	REST	chr11:66885865-66887319	H1-neurons	neurons:	n/a	chr11:66886843-66886851 chr11:66886288-66886301 chr11:66886613-66886626
40	POLR2A	chr11:66885885-66885964	MCF-7	breast:	n/a	n/a
41	TAF1	chr11:66885578-66886216	H1-hESC	embryonic stem cell:	n/a	n/a
42	STAT5A	chr11:66885681-66886166	GM12878	blood:	n/a	chr11:66885854-66885866
43	POLR2A	chr11:66885163-66887241	GM19099	blood:	n/a	n/a
44	BACH1	chr11:66885141-66886766	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr11:66885377-66886246	GM12891	blood:	n/a	n/a
46	POLR2A	chr11:66885589-66886158	GM12892	blood:	n/a	n/a
47	MAX	chr11:66885841-66887070	A549	lung:	n/a	chr11:66886120-66886129 chr11:66886002-66886011
48	POLR2A	chr11:66885063-66886246	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr11:66885923-66887424	MCF-7	breast:	n/a	n/a
50	POLR2A	chr11:66885089-66887088	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66884866..66886450-chr11:67007040..67008886,2	MCF-7	breast:
2	chr11:66885940..66887950-chr11:67395860..67397869,2	K562	blood:
3	chr11:66884756..66886465-chr11:66946415..66948664,2	MCF-7	breast:
4	chr11:66885437..66888305-chr11:67055921..67058495,2	MCF-7	breast:
5	chr11:66821625..66825972-chr11:66885437..66888104,7	MCF-7	breast:
6	chr11:66885158..66886682-chr11:67030764..67032501,2	K562	blood:
7	chr11:66885002..66889173-chr11:67005085..67009324,11	K562	blood:
8	chr11:66884916..66890908-chr11:67005112..67010354,8	MCF-7	breast:
9	chr11:66821404..66826403-chr11:66884710..66889541,16	MCF-7	breast:
10	chr11:66883623..66889678-chr11:67005085..67009894,16	K562	blood:
11	chr11:66847793..66850553-chr11:66883657..66886437,2	MCF-7	breast:

Variant related genes	Relation type
KDM2A	TF binding region
ENSG00000167799	Chromatin interaction
ENSG00000173156	Chromatin interaction
ENSG00000172932	Chromatin interaction
ENSG00000173120	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	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	esv3412807	chr11:66884326-66888124	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv3397435	chr11:66884601-66887149	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv3400268	chr11:66884676-66888099	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3328460	chr11:66884901-66888249	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66881000-66886800	Weak transcription	K562	blood
2	chr11:66883600-66886000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:66884800-66886200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:66884800-66888800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr11:66884800-66889200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr11:66885000-66886000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:66885000-66886000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr11:66885000-66886200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr11:66885000-66886200	Bivalent/Poised TSS	Thymus	Thymus
10	chr11:66885000-66886800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:66885000-66887200	Weak transcription	Fetal Brain Male	brain
12	chr11:66885000-66888600	Active TSS	Brain Substantia Nigra	brain
13	chr11:66885000-66888800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:66885000-66888800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:66885000-66889000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:66885000-66889000	Active TSS	Lung	lung
17	chr11:66885000-66889000	Active TSS	Osteobl	bone
18	chr11:66885000-66889200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr11:66885000-66889600	Active TSS	Psoas Muscle	Psoas
20	chr11:66885000-66889800	Active TSS	Fetal Brain Female	brain
21	chr11:66885000-66889800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr11:66885200-66886000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:66885200-66886000	Weak transcription	Hela-S3	cervix
24	chr11:66885200-66886200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:66885200-66886200	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr11:66885200-66886200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:66885200-66886800	Weak transcription	Fetal Kidney	kidney
28	chr11:66885200-66887400	Weak transcription	Fetal Heart	heart
29	chr11:66885200-66887600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:66885200-66887800	Active TSS	Spleen	Spleen
31	chr11:66885200-66888000	Active TSS	Primary T cells from cord blood	blood
32	chr11:66885200-66888400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:66885200-66888400	Active TSS	Brain Cingulate Gyrus	brain
34	chr11:66885200-66888400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:66885200-66888600	Active TSS	Duodenum Mucosa	Duodenum
36	chr11:66885200-66888600	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr11:66885200-66888800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr11:66885200-66888800	Active TSS	Esophagus	oesophagus
39	chr11:66885200-66888800	Active TSS	Gastric	stomach
40	chr11:66885200-66889000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr11:66885200-66889000	Active TSS	H9 Cell Line	embryonic stem cell
42	chr11:66885200-66889000	Active TSS	Brain Angular Gyrus	brain
43	chr11:66885200-66889000	Active TSS	Colon Smooth Muscle	Colon
44	chr11:66885200-66889000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr11:66885200-66889200	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr11:66885200-66889200	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr11:66885200-66889200	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr11:66885200-66889400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr11:66885200-66889400	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr11:66885200-66889400	Active TSS	Brain Hippocampus Middle	brain

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