Variant report

Variant	rs539986537
Chromosome Location	chr11:58939261-58939262
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	RELA	chr11:58938906-58939772	GM19099	blood:	n/a	n/a
2	SIN3A	chr11:58938945-58942122	H1-hESC	embryonic stem cell:	n/a	chr11:58939520-58939533 chr11:58941266-58941279
3	RAD21	chr11:58938811-58939703	A549	lung:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
4	NFATC1	chr11:58938785-58939830	GM12878	blood:	n/a	n/a
5	RAD21	chr11:58938812-58939690	Hela-S3	cervix:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
6	MTA3	chr11:58938544-58939888	GM12878	blood:	n/a	n/a
7	CCNT2	chr11:58938942-58940172	K562	blood:	n/a	chr11:58939582-58939591 chr11:58939560-58939569
8	MAX	chr11:58938910-58939793	K562	blood:	n/a	chr11:58939511-58939521
9	SMARCB1	chr11:58939077-58941966	Hela-S3	cervix:	n/a	n/a
10	POU2F2	chr11:58938873-58941108	GM12878	blood:	n/a	chr11:58940304-58940316 chr11:58939780-58939798 chr11:58939563-58939575 chr11:58940301-58940313 chr11:58939785-58939792 chr11:58939784-58939794 chr11:58939104-58939116 chr11:58939784-58939793
11	RAD21	chr11:58938727-58939747	IMR90	lung:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
12	ELF1	chr11:58938897-58939332	MCF-7	breast:	n/a	n/a
13	UBTF	chr11:58938984-58939703	K562	blood:	n/a	n/a
14	YY1	chr11:58939225-58939819	GM12891	blood:	n/a	n/a
15	JUN	chr11:58939061-58939526	H1-hESC	embryonic stem cell:	n/a	chr11:58939492-58939501
16	CTCF	chr11:58938362-58940223	SK-N-SH	brain:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
17	POLR2A	chr11:58938795-58945281	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:58938963-58941106	GM19099	blood:	n/a	n/a
19	TBL1XR1	chr11:58938955-58939531	K562	blood:	n/a	n/a
20	RAD21	chr11:58938897-58939661	GM12878	blood:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079
21	CUX1	chr11:58938854-58939567	GM12878	blood:	n/a	n/a
22	MAX	chr11:58938986-58939821	SK-N-SH	brain:	n/a	chr11:58939511-58939521
23	SMC3	chr11:58938856-58939661	HepG2	liver:	n/a	chr11:58939069-58939079 chr11:58939103-58939117 chr11:58939065-58939079
24	MAX	chr11:58938768-58940390	A549	lung:	n/a	chr11:58939511-58939521
25	SP1	chr11:58938841-58939717	A549	lung:	n/a	chr11:58939110-58939120 chr11:58939581-58939593 chr11:58939582-58939591 chr11:58939110-58939120
26	BHLHE40	chr11:58938960-58939774	HepG2	liver:	n/a	n/a
27	TBL1XR1	chr11:58938940-58939639	K562	blood:	n/a	n/a
28	E2F6	chr11:58939137-58939848	K562	blood:	n/a	chr11:58939440-58939449
29	POLR2A	chr11:58939063-58939285	Hela-S3	cervix:	n/a	n/a
30	MAX	chr11:58938887-58939779	NB4	blood:	n/a	chr11:58939511-58939521
31	TCF12	chr11:58938800-58939777	A549	lung:	n/a	chr11:58939063-58939073
32	CTCF	chr11:58938809-58939263	K562	blood:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939068-58939078
33	RFX5	chr11:58938949-58939512	GM12878	blood:	n/a	n/a
34	EP300	chr11:58938926-58939830	ECC-1	luminal epithelium:	n/a	chr11:58939305-58939319 chr11:58939440-58939449
35	POLR2A	chr11:58938940-58939899	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr11:58939087-58942313	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:58939132-58939292	A549	lung:	n/a	n/a
38	CTCF	chr11:58938906-58939682	GM19238	blood:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
39	CTCF	chr11:58938924-58939720	H1-hESC	embryonic stem cell:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939508-58939521 chr11:58939068-58939078
40	MAZ	chr11:58938904-58940204	Hela-S3	cervix:	n/a	chr11:58939511-58939521
41	BRCA1	chr11:58938948-58939572	H1-hESC	embryonic stem cell:	n/a	n/a
42	ZNF143	chr11:58938874-58939764	K562	blood:	n/a	chr11:58939440-58939450
43	MYC	chr11:58938923-58939709	H1-hESC	embryonic stem cell:	n/a	chr11:58939511-58939521
44	NRF1	chr11:58938864-58939279	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr11:58938854-58939885	GM12892	blood:	n/a	n/a
46	POLR2A	chr11:58939192-58941003	GM18505	blood:	n/a	n/a
47	POLR2A	chr11:58938860-58941234	GM12892	blood:	n/a	n/a
48	MAZ	chr11:58938731-58942643	IMR90	lung:	n/a	chr11:58939511-58939521 chr11:58942531-58942541
49	CTCF	chr11:58938905-58939309	Gliobla	brain:	n/a	chr11:58939063-58939081 chr11:58939066-58939079 chr11:58939066-58939075 chr11:58939106-58939116 chr11:58939064-58939080 chr11:58939068-58939078
50	RAD21	chr11:58938700-58939692	A549	lung:	n/a	chr11:58939067-58939080 chr11:58939064-58939083 chr11:58939507-58939521 chr11:58939065-58939079 chr11:58939069-58939079

No.	Distal block	Cell Line	Cell type
1	chr11:58939007..58939939-chr11:58975144..58976495,4	MCF-7	breast:
2	chr11:58938973..58939965-chr11:59447518..59448398,3	K562	blood:
3	chr11:58938934..58939576-chr11:59051413..59052308,3	MCF-7	breast:
4	chr11:58343237..58345881-chr11:58936566..58939542,2	K562	blood:
5	chr11:58939119..58939626-chr11:58968685..58969428,2	K562	blood:
6	chr11:58939029..58939641-chr11:58968515..58969414,2	MCF-7	breast:

Variant related genes	Relation type
DTX4	TF binding region
ENSG00000110031	Chromatin interaction
ENSG00000214797	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv3427190	chr11:58938601-58941149	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3399192	chr11:58938776-58941074	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 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	chr11:58938600-58942000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:58938800-58939400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
3	chr11:58938800-58939400	Enhancers	Fetal Brain Male	brain
4	chr11:58938800-58939800	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr11:58938800-58939800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:58938800-58940200	Active TSS	H1 Cell Line	embryonic stem cell
7	chr11:58938800-58940200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr11:58938800-58940200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr11:58938800-58940200	Active TSS	Primary T cells from cord blood	blood
10	chr11:58938800-58940200	Active TSS	Brain Angular Gyrus	brain
11	chr11:58938800-58940200	Active TSS	Brain Germinal Matrix	brain
12	chr11:58938800-58940200	Active TSS	Fetal Brain Female	brain
13	chr11:58938800-58940400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr11:58938800-58940400	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr11:58938800-58940400	Active TSS	Brain Hippocampus Middle	brain
16	chr11:58938800-58941200	Active TSS	Brain Cingulate Gyrus	brain
17	chr11:58938800-58941400	Active TSS	Brain Anterior Caudate	brain
18	chr11:58938800-58941800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr11:58939000-58939400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:58939000-58939400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr11:58939000-58939400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr11:58939000-58939400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr11:58939000-58939400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:58939000-58939400	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr11:58939000-58939400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr11:58939000-58939400	Active TSS	Thymus	Thymus
27	chr11:58939000-58939400	Flanking Active TSS	Dnd41	blood
28	chr11:58939000-58939400	Flanking Active TSS	HMEC	breast
29	chr11:58939000-58939400	Flanking Active TSS	NHEK	skin
30	chr11:58939000-58939600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr11:58939000-58939600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr11:58939000-58939600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:58939000-58939600	Flanking Active TSS	Liver	Liver
34	chr11:58939000-58939600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
35	chr11:58939000-58939600	Active TSS	Stomach Smooth Muscle	stomach
36	chr11:58939000-58939600	Bivalent/Poised TSS	NH-A	brain
37	chr11:58939000-58939800	Active TSS	K562	blood
38	chr11:58939000-58940000	Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr11:58939000-58940000	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr11:58939000-58940000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr11:58939000-58940000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:58939000-58940000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:58939000-58940000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:58939000-58940000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:58939000-58940000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:58939000-58940000	Active TSS	Pancreas	Pancrea
47	chr11:58939000-58940000	Active TSS	Right Ventricle	heart
48	chr11:58939000-58940000	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr11:58939000-58940000	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr11:58939000-58940000	Active TSS	Osteobl	bone

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