Variant report

Variant	rs10166997
Chromosome Location	chr2:11270051-11270052
allele	C/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	SP1	chr2:11269782-11270519	A549	lung:	n/a	chr2:11270023-11270035 chr2:11270135-11270144 chr2:11270155-11270166 chr2:11270157-11270166 chr2:11270134-11270146 chr2:11270024-11270033 chr2:11270134-11270145 chr2:11270134-11270146 chr2:11270094-11270103 chr2:11270156-11270165 chr2:11270131-11270145 chr2:11270155-11270167 chr2:11270023-11270035 chr2:11270155-11270167 chr2:11270173-11270184 chr2:11270092-11270104 chr2:11270156-11270166 chr2:11270156-11270166 chr2:11270136-11270145 chr2:11270092-11270104 chr2:11270152-11270166
2	MAX	chr2:11269751-11270463	H1-hESC	embryonic stem cell:	n/a	chr2:11270156-11270166
3	MAX	chr2:11270001-11270331	HepG2	liver:	n/a	chr2:11270156-11270166
4	ZEB1	chr2:11270014-11270244	GM12878	blood:	n/a	chr2:11270205-11270214
5	POLR2A	chr2:11269971-11270288	A549	lung:	n/a	n/a
6	EP300	chr2:11270011-11270371	H1-hESC	embryonic stem cell:	n/a	chr2:11270165-11270181
7	E2F6	chr2:11269597-11270581	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:11269902-11270300	HepG2	liver:	n/a	n/a
9	ELF1	chr2:11269973-11270358	HepG2	liver:	n/a	chr2:11270145-11270158
10	STAT3	chr2:11269918-11270322	MCF10A-Er-Src	breast:	n/a	chr2:11270263-11270275
11	CTCF	chr2:11269588-11270577	SK-N-SH	brain:	n/a	n/a
12	MYBL2	chr2:11269933-11270610	HepG2	liver:	n/a	n/a
13	CTCF	chr2:11270025-11270420	A549	lung:	n/a	n/a
14	POLR2A	chr2:11269894-11270398	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr2:11269923-11270531	MCF-7	breast:	n/a	n/a
16	ELF1	chr2:11269874-11270503	MCF-7	breast:	n/a	chr2:11270145-11270158
17	ELF1	chr2:11269853-11270513	MCF-7	breast:	n/a	chr2:11270145-11270158
18	CTCF	chr2:11269973-11270569	A549	lung:	n/a	n/a
19	MAX	chr2:11269737-11270570	A549	lung:	n/a	chr2:11270156-11270166
20	ELF1	chr2:11269847-11270285	K562	blood:	n/a	chr2:11270145-11270158
21	HDAC2	chr2:11269899-11270406	HepG2	liver:	n/a	chr2:11270035-11270054
22	GABPA	chr2:11269985-11270280	HepG2	liver:	n/a	chr2:11270077-11270091 chr2:11270156-11270165
23	CTCF	chr2:11269980-11270130	NHDF-neo	bronchial:	n/a	n/a
24	CEBPD	chr2:11269983-11270282	HepG2	liver:	n/a	n/a
25	BHLHE40	chr2:11269749-11270391	K562	blood:	n/a	n/a
26	RAD21	chr2:11269884-11270611	A549	lung:	n/a	chr2:11270232-11270246
27	POLR2A	chr2:11269887-11270478	HCT-116	colon:	n/a	n/a
28	E2F6	chr2:11269755-11270482	H1-hESC	embryonic stem cell:	n/a	n/a
29	SMC3	chr2:11270033-11270439	K562	blood:	n/a	n/a
30	STAT3	chr2:11269973-11270287	MCF10A-Er-Src	breast:	n/a	chr2:11270263-11270275
31	CTCF	chr2:11270041-11270420	K562	blood:	n/a	n/a
32	MAX	chr2:11269746-11270414	NB4	blood:	n/a	chr2:11270156-11270166
33	MYC	chr2:11270028-11270416	K562	blood:	n/a	chr2:11270156-11270166
34	CTCF	chr2:11270050-11270514	K562	blood:	n/a	n/a
35	YY1	chr2:11269998-11270348	HCT-116	colon:	n/a	n/a
36	E2F6	chr2:11269872-11270417	K562	blood:	n/a	n/a
37	E2F6	chr2:11269979-11270386	K562	blood:	n/a	n/a
38	CTCF	chr2:11270048-11270456	K562	blood:	n/a	n/a
39	TAF1	chr2:11269894-11270586	ECC-1	luminal epithelium:	n/a	n/a
40	TBP	chr2:11269988-11270360	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr2:11269859-11270606	ECC-1	luminal epithelium:	n/a	n/a
42	CTCF	chr2:11270051-11270406	K562	blood:	n/a	n/a
43	RAD21	chr2:11269825-11270534	ECC-1	luminal epithelium:	n/a	chr2:11270232-11270246
44	POLR2A	chr2:11269902-11270336	MCF-7	breast:	n/a	n/a
45	CTCF	chr2:11270020-11270170	HVMF	connective:	n/a	n/a
46	EP300	chr2:11269702-11270323	K562	blood:	n/a	chr2:11270165-11270181
47	MXI1	chr2:11269953-11270354	HepG2	liver:	n/a	n/a
48	RAD21	chr2:11270025-11270413	H1-hESC	embryonic stem cell:	n/a	chr2:11270232-11270246
49	SP4	chr2:11269962-11270469	H1-hESC	embryonic stem cell:	n/a	chr2:11270155-11270166 chr2:11270134-11270145 chr2:11270173-11270184 chr2:11270151-11270167 chr2:11270130-11270146 chr2:11270153-11270169 chr2:11270021-11270037 chr2:11270023-11270039
50	CEBPB	chr2:11270044-11270438	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11213310..11214023-chr2:11269749..11271029,3	MCF-7	breast:
2	chr2:11268656..11272146-chr2:11621524..11625212,4	MCF-7	breast:
3	chr2:11269743..11271630-chr2:11718749..11720489,2	K562	blood:
4	chr2:11256745..11259166-chr2:11268609..11271261,2	MCF-7	breast:
5	chr2:11268242..11270233-chr2:11636174..11639118,2	MCF-7	breast:
6	chr2:11267451..11270365-chr2:11623207..11626147,3	MCF-7	breast:
7	chr2:10954337..10955272-chr2:11269771..11270646,2	MCF-7	breast:
8	chr2:10973920..10977755-chr2:11268417..11271773,4	K562	blood:
9	chr2:11268985..11271402-chr2:11299866..11302582,2	MCF-7	breast:
10	chr2:10952686..10954335-chr2:11268675..11270321,2	MCF-7	breast:
11	chr2:11259687..11261263-chr2:11269036..11270922,2	MCF-7	breast:
12	chr2:10972241..10973183-chr2:11269753..11270676,4	MCF-7	breast:
13	chr2:11267717..11270213-chr2:11295348..11297264,2	MCF-7	breast:
14	chr2:10828291..10832221-chr2:11269738..11273006,3	MCF-7	breast:
15	chr2:10947754..10949615-chr2:11268944..11271404,2	MCF-7	breast:
16	chr2:11256796..11258372-chr2:11268716..11271712,2	MCF-7	breast:
17	chr2:11269728..11273923-chr2:11678087..11684060,5	MCF-7	breast:
18	chr2:11268781..11271760-chr2:11481751..11485237,3	MCF-7	breast:
19	chr2:10849480..10850065-chr2:11269811..11270311,2	MCF-7	breast:
20	chr2:10972556..10974253-chr2:11268558..11270132,2	MCF-7	breast:
21	chr2:11239238..11239846-chr2:11269978..11270598,2	MCF-7	breast:
22	chr2:10971180..10977465-chr2:11267266..11272931,15	MCF-7	breast:
23	chr2:10972286..10973137-chr2:11269666..11270590,6	MCF-7	breast:

Variant related genes	Relation type
C2orf50	TF binding region
ENSG00000115761	Chromatin interaction
ENSG00000134318	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000162976	Chromatin interaction
ENSG00000264010	Chromatin interaction
ENSG00000243819	Chromatin interaction
ENSG00000143870	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10166950	0.95[EUR][1000 genomes]
rs10191933	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs10495579	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11676318	0.89[EUR][1000 genomes]
rs11681385	0.89[EUR][1000 genomes]
rs13392854	0.90[EUR][1000 genomes]
rs2357991	0.98[EUR][1000 genomes]
rs28433865	0.90[EUR][1000 genomes]
rs55935965	0.90[EUR][1000 genomes]
rs72785428	0.95[EUR][1000 genomes]
rs72785429	0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11268400-11270600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:11268400-11270600	Enhancers	NH-A	brain
3	chr2:11268600-11270200	Enhancers	NHDF-Ad	bronchial
4	chr2:11268800-11270200	Weak transcription	Spleen	Spleen
5	chr2:11269000-11270200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:11269200-11270200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:11269200-11270800	Enhancers	HUVEC	blood vessel
8	chr2:11269600-11270200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:11269600-11270200	Enhancers	Brain Substantia Nigra	brain
10	chr2:11269600-11270200	Active TSS	Thymus	Thymus
11	chr2:11269600-11270400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr2:11269600-11270400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:11269600-11270400	Active TSS	Fetal Brain Female	brain
14	chr2:11269600-11270400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr2:11269600-11270600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr2:11269600-11270600	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr2:11269600-11270600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr2:11269600-11270600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:11269600-11270600	Enhancers	Lung	lung
20	chr2:11269600-11270600	Flanking Active TSS	K562	blood
21	chr2:11269600-11270800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr2:11269600-11270800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr2:11269600-11270800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:11269600-11270800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:11269600-11270800	Enhancers	Fetal Heart	heart
26	chr2:11269600-11271000	Flanking Active TSS	Dnd41	blood
27	chr2:11269800-11270200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr2:11269800-11270200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:11269800-11270200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:11269800-11270200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:11269800-11270200	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:11269800-11270200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr2:11269800-11270200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr2:11269800-11270200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:11269800-11270200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:11269800-11270200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:11269800-11270200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr2:11269800-11270200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr2:11269800-11270200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr2:11269800-11270200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr2:11269800-11270200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:11269800-11270200	Active TSS	Esophagus	oesophagus
43	chr2:11269800-11270200	Active TSS	Fetal Intestine Large	intestine
44	chr2:11269800-11270200	Active TSS	Fetal Thymus	thymus
45	chr2:11269800-11270200	Active TSS	Gastric	stomach
46	chr2:11269800-11270200	Active TSS	Ovary	ovary
47	chr2:11269800-11270200	Active TSS	NHEK	skin
48	chr2:11269800-11270200	Active TSS	Osteobl	bone
49	chr2:11269800-11270400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:11269800-11270400	Active TSS	H9 Cell Line	embryonic stem cell

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