Variant report

Variant	rs643949
Chromosome Location	chr11:64684283-64684284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64683864-64685262	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr11:64684268-64685329	HUVEC	blood vessel:	n/a	n/a
3	MXI1	chr11:64683557-64685214	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr11:64684275-64685347	HUVEC	blood vessel:	n/a	n/a
5	MXI1	chr11:64683651-64685147	HepG2	liver:	n/a	n/a
6	MXI1	chr11:64683493-64686214	SK-N-SH	brain:	n/a	n/a
7	SMARCC1	chr11:64683344-64684789	Hela-S3	cervix:	n/a	n/a
8	MAX	chr11:64684186-64685148	ECC-1	luminal epithelium:	n/a	n/a
9	RUNX3	chr11:64683714-64684323	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:64683716-64684299	HL-60	blood:	n/a	n/a
11	POLR2A	chr11:64684276-64684843	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:64682720-64685449	Hela-S3	cervix:	n/a	n/a
13	SMC3	chr11:64684192-64684357	K562	blood:	n/a	n/a
14	MAX	chr11:64683714-64684341	HepG2	liver:	n/a	chr11:64683992-64684008 chr11:64683765-64683775
15	MAX	chr11:64683433-64685238	HepG2	liver:	n/a	chr11:64683992-64684008 chr11:64683765-64683775
16	HEY1	chr11:64683309-64685509	K562	blood:	n/a	n/a
17	CBX3	chr11:64684030-64685220	K562	blood:	n/a	n/a
18	TAF1	chr11:64684246-64684941	H1-neurons	neurons:	n/a	n/a
19	MAX	chr11:64683309-64685177	K562	blood:	n/a	chr11:64683992-64684008 chr11:64683765-64683775
20	PML	chr11:64683744-64684921	GM12878	blood:	n/a	n/a
21	CREB1	chr11:64683600-64685290	HepG2	liver:	n/a	n/a
22	CHD1	chr11:64683915-64684823	GM12878	blood:	n/a	chr11:64684690-64684700
23	TCF12	chr11:64684154-64685403	A549	lung:	n/a	chr11:64685114-64685123
24	POLR2A	chr11:64684276-64684894	MCF-7	breast:	n/a	n/a
25	POLR2A	chr11:64684246-64685157	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr11:64683585-64685210	HepG2	liver:	n/a	n/a
27	ETS1	chr11:64684236-64684772	K562	blood:	n/a	n/a
28	POLR2A	chr11:64683694-64685131	IMR90	lung:	n/a	n/a
29	CHD1	chr11:64683200-64685890	IMR90	lung:	n/a	chr11:64684690-64684700
30	HCFC1	chr11:64682583-64686155	Hela-S3	cervix:	n/a	n/a
31	ELF1	chr11:64683425-64684997	GM12878	blood:	n/a	n/a
32	SIN3AK20	chr11:64683477-64685075	K562	blood:	n/a	n/a
33	SIN3AK20	chr11:64683551-64685268	PANC-1	pancreas:	n/a	n/a
34	REST	chr11:64683994-64685180	H1-neurons	neurons:	n/a	chr11:64684692-64684705
35	POLR2A	chr11:64684179-64685372	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr11:64684082-64685248	ECC-1	luminal epithelium:	n/a	n/a
37	UBTF	chr11:64683651-64685361	K562	blood:	n/a	n/a
38	POLR2A	chr11:64683708-64685155	GM12892	blood:	n/a	n/a
39	POLR2A	chr11:64684281-64685225	PANC-1	pancreas:	n/a	n/a
40	MAX	chr11:64684262-64685549	ECC-1	luminal epithelium:	n/a	n/a
41	NR2F2	chr11:64683287-64685215	MCF-7	breast:	n/a	n/a
42	POLR2A	chr11:64683371-64685040	Hela-S3	cervix:	n/a	n/a
43	SIN3A	chr11:64683484-64685248	H1-hESC	embryonic stem cell:	n/a	chr11:64683964-64683978
44	MXI1	chr11:64683562-64685895	IMR90	lung:	n/a	n/a
45	CHD1	chr11:64684233-64684827	H1-hESC	embryonic stem cell:	n/a	chr11:64684690-64684700
46	MXI1	chr11:64683689-64685563	GM12878	blood:	n/a	n/a
47	CTCF	chr11:64684280-64684430	AG04449	skin:	n/a	n/a
48	BCL3	chr11:64684282-64684776	A549	lung:	n/a	chr11:64684346-64684359
49	POLR2A	chr11:64683338-64684873	K562	blood:	n/a	n/a
50	MTA3	chr11:64683389-64684814	GM12878	blood:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64683710..64686843-chr11:64689150..64693843,9	MCF-7	breast:
2	chr11:64683667..64685834-chr11:64900771..64903507,2	K562	blood:
3	chr11:64683875..64684962-chr7:44836077..44837040,3	Hela-S3	cervix:
4	chr11:64683512..64686373-chr11:64701129..64703249,2	MCF-7	breast:
5	chr11:64644179..64646943-chr11:64683100..64687957,8	MCF-7	breast:
6	chr11:64684246..64684996-chr20:47894716..47895670,2	Hela-S3	cervix:
7	chr11:64683337..64686600-chr11:64690985..64694112,6	MCF-7	breast:
8	chr11:64659914..64665589-chr11:64679566..64685622,11	K562	blood:
9	chr11:64684182..64687060-chr11:64693697..64696129,2	K562	blood:
10	chr11:64644503..64648099-chr11:64683052..64686363,9	K562	blood:
11	chr1:33815262..33815912-chr11:64684138..64685054,2	Hela-S3	cervix:
12	chr11:64651561..64659485-chr11:64681552..64686807,18	K562	blood:
13	chr11:64682623..64685328-chr11:64870943..64873387,2	MCF-7	breast:
14	chr11:64681545..64685255-chr11:64700864..64703818,3	K562	blood:
15	chr11:64684202..64684798-chr5:171433854..171434422,2	Hela-S3	cervix:
16	chr11:64544525..64547813-chr11:64683284..64685866,4	K562	blood:
17	chr11:64653740..64655395-chr11:64682265..64684591,2	MCF-7	breast:
18	chr11:64681819..64686102-chr11:64779905..64782957,5	MCF-7	breast:
19	chr11:64683021..64685981-chr11:64781625..64784265,4	MCF-7	breast:
20	chr11:64664073..64665620-chr11:64682984..64684733,2	MCF-7	breast:
21	chr11:64646527..64648346-chr11:64683617..64685265,2	MCF-7	breast:
22	chr11:64644520..64646273-chr11:64683342..64685362,3	MCF-7	breast:
23	chr11:64683299..64686210-chr11:64705910..64707683,2	K562	blood:
24	chr11:64682540..64686355-chr11:64876478..64880305,4	K562	blood:
25	chr11:64543951..64548420-chr11:64681372..64686852,8	K562	blood:
26	chr11:64682450..64685608-chr11:64808232..64811277,3	MCF-7	breast:
27	chr11:64681631..64684611-chr11:64749836..64752402,2	K562	blood:
28	chr11:64682424..64684524-chr11:64927254..64929359,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPP2R5B	TF binding region
ATG2A	TF binding region
ENSG00000267804	Chromatin interaction
ENSG00000168070	Chromatin interaction
ENSG00000134686	Chromatin interaction
ENSG00000177410	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000110046	Chromatin interaction
ENSG00000168061	Chromatin interaction
ENSG00000229719	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000149735	Chromatin interaction
ENSG00000203400	Chromatin interaction
ENSG00000209042	Chromatin interaction
ENSG00000124201	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000196262	Chromatin interaction
ENSG00000072803	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000255058	Chromatin interaction
ENSG00000162298	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000207648	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11827610	0.83[EUR][1000 genomes]
rs12286941	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35079323	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35115827	0.86[EUR][1000 genomes]
rs3867127	0.80[EUR][1000 genomes]
rs57365630	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57393537	0.94[EUR][1000 genomes]
rs59677833	0.83[EUR][1000 genomes]
rs60711419	0.86[EUR][1000 genomes]
rs60798873	0.94[EUR][1000 genomes]
rs61024397	0.94[EUR][1000 genomes]
rs61741079	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61742063	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs628595	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs646778	0.86[AFR][1000 genomes]
rs647489	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs664997	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7102350	0.83[EUR][1000 genomes]
rs7113751	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7942472	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs885999	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
2	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
3	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription 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	1071 gene(s)	inside rSNPs	diseases
4	nsv897704	chr11:64584987-64701030	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
5	nsv897705	chr11:64591679-64701030	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS 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	1028 gene(s)	inside rSNPs	diseases
6	nsv897706	chr11:64591679-64721908	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
7	nsv897707	chr11:64600002-64701030	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
8	nsv897708	chr11:64602757-64695271	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1028 gene(s)	inside rSNPs	diseases
9	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
10	nsv555208	chr11:64645119-64771179	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1029 gene(s)	inside rSNPs	diseases
11	nsv555209	chr11:64661532-64684288	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64683000-64684600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:64683200-64684400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr11:64683200-64684400	Flanking Active TSS	Colonic Mucosa	Colon
4	chr11:64683200-64684400	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr11:64683200-64684400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr11:64683200-64684600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr11:64683200-64684600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr11:64683400-64684400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr11:64683400-64684400	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr11:64683400-64684400	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr11:64683400-64684400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr11:64683400-64684400	Flanking Active TSS	Fetal Thymus	thymus
13	chr11:64683400-64684400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr11:64683400-64684400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr11:64683400-64684400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr11:64683400-64684600	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr11:64683400-64684600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr11:64683400-64684600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:64683400-64684600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr11:64683400-64685400	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr11:64683400-64685600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr11:64683400-64685800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr11:64683600-64684400	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr11:64683600-64684400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr11:64683600-64684400	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr11:64683600-64684400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr11:64683600-64684600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:64683600-64684600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:64683600-64684600	Flanking Active TSS	Fetal Brain Male	brain
30	chr11:64683600-64685200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr11:64683600-64685400	Active TSS	A549	lung
32	chr11:64683600-64685600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr11:64683600-64685800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:64683800-64684800	Active TSS	Gastric	stomach
35	chr11:64683800-64685000	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr11:64683800-64685000	Active TSS	Hela-S3	cervix
37	chr11:64683800-64685200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:64683800-64685200	Active TSS	Fetal Kidney	kidney
39	chr11:64683800-64685200	Active TSS	Thymus	Thymus
40	chr11:64683800-64685200	Active TSS	NHDF-Ad	bronchial
41	chr11:64683800-64685400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr11:64683800-64685400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:64683800-64685400	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr11:64683800-64685400	Active TSS	Placenta Amnion	Placenta Amnion
45	chr11:64683800-64685400	Active TSS	NHLF	lung
46	chr11:64683800-64685600	Active TSS	Aorta	Aorta
47	chr11:64683800-64685800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr11:64683800-64686000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr11:64684000-64684600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:64684000-64684600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

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