Variant report

Variant	rs140387708
Chromosome Location	chr2:55462584-55462585
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55458744-55464800	K562	blood:	n/a	n/a
2	POLR2A	chr2:55462090-55464756	U87	brain:	n/a	n/a
3	POLR2A	chr2:55462068-55462624	U87	brain:	n/a	n/a
4	POLR2A	chr2:55462401-55465841	HepG2	liver:	n/a	n/a
5	CTCF	chr2:55462551-55462749	T-47D	breast:	n/a	n/a
6	POLR2A	chr2:55458959-55464692	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
8	POLR2A	chr2:55462162-55463984	GM12891	blood:	n/a	n/a
9	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
10	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:55462398-55463833	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr2:55458760-55464736	HepG2	liver:	n/a	n/a
14	POLR2A	chr2:55462418-55462678	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:55461373-55464681	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:55459164-55464717	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:55458775-55464779	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr2:55462453-55462897	K562	blood:	n/a	n/a
19	POLR2A	chr2:55458974-55464629	K562	blood:	n/a	n/a
20	POLR2A	chr2:55458800-55464614	K562	blood:	n/a	n/a
21	HEY1	chr2:55462435-55463896	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:55462208-55464000	H1-hESC	embryonic stem cell:	n/a	n/a
23	HEY1	chr2:55462185-55464659	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:55458988-55464662	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:55461469-55464573	K562	blood:	n/a	n/a
26	POLR2A	chr2:55462436-55462680	ProgFib	skin:	n/a	n/a
27	POLR2A	chr2:55458860-55465354	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr2:55458989-55464724	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr2:55458966-55464603	GM12892	blood:	n/a	n/a
30	POLR2A	chr2:55459024-55464715	GM18505	blood:	n/a	n/a
31	POLR2A	chr2:55462273-55464697	HUVEC	blood vessel:	n/a	n/a
32	ZBTB33	chr2:55462440-55462756	K562	blood:	n/a	n/a
33	POLR2A	chr2:55458733-55465490	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr2:55461687-55462658	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr2:55458865-55465521	MCF-7	breast:	n/a	n/a
36	POLR2A	chr2:55460323-55464639	A549	lung:	n/a	n/a
37	POLR2A	chr2:55458817-55464677	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:55461565-55464760	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr2:55462494-55462717	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:55458685-55467019	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr2:55459009-55464639	GM12892	blood:	n/a	n/a
42	POLR2A	chr2:55459696-55465435	K562	blood:	n/a	n/a
43	POLR2A	chr2:55458747-55464854	U87	brain:	n/a	n/a
44	HEY1	chr2:55462426-55463160	K562	blood:	n/a	n/a
45	POLR2A	chr2:55462221-55464718	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr2:55458947-55464599	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr2:55461354-55464525	GM12891	blood:	n/a	n/a
48	POLR2A	chr2:55461854-55463961	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr2:55458451-55467274	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr2:55458733-55464641	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55228095..55231014-chr2:55462298..55463930,2	MCF-7	breast:
2	chr2:55462241..55464416-chr2:55656583..55659722,3	MCF-7	breast:
3	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
4	chr2:55461063..55464036-chr2:55678930..55681673,2	MCF-7	breast:
5	chr2:55462245..55463992-chr2:55494868..55496568,2	K562	blood:
6	chr2:55313997..55316994-chr2:55461231..55462844,2	K562	blood:

No data

Variant related genes	Relation type
CLHC1	TF binding region
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv961777	chr2:55461976-55463347	Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Active TSS Enhancers	TF binding region Chromatin interactive region miRNA target site	7 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	chr2:55460000-55463000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
2	chr2:55460000-55463400	Transcr. at gene 5' and 3'	K562	blood
3	chr2:55460200-55462600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
4	chr2:55460200-55463000	Transcr. at gene 5' and 3'	A549	lung
5	chr2:55460400-55462600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
6	chr2:55460400-55462600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:55460400-55463000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:55460600-55462600	Weak transcription	Aorta	Aorta
9	chr2:55460600-55463400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:55460600-55463800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
11	chr2:55460800-55462600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
12	chr2:55460800-55462600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
13	chr2:55461000-55462600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55461000-55462800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr2:55461000-55463000	Genic enhancers	Brain Germinal Matrix	brain
16	chr2:55461000-55463000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:55461000-55464600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:55461000-55470200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:55461200-55462600	Genic enhancers	NHDF-Ad	bronchial
20	chr2:55461200-55462800	Weak transcription	Pancreas	Pancrea
21	chr2:55461200-55463000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:55461200-55463000	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr2:55461200-55463200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr2:55461200-55463200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
25	chr2:55461200-55463600	Strong transcription	Rectal Smooth Muscle	rectum
26	chr2:55461200-55463600	Strong transcription	Thymus	Thymus
27	chr2:55461200-55464600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:55461200-55464800	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:55461400-55463000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr2:55461400-55463000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:55461400-55463400	Strong transcription	Ovary	ovary
32	chr2:55461400-55463600	Strong transcription	Brain Substantia Nigra	brain
33	chr2:55461400-55464000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:55461400-55464400	Strong transcription	Brain Anterior Caudate	brain
35	chr2:55461400-55464400	Strong transcription	Fetal Lung	lung
36	chr2:55461400-55466600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:55461400-55477600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:55461600-55462800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:55461600-55462800	Strong transcription	Fetal Brain Female	brain
40	chr2:55461600-55463000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:55461600-55463200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:55461600-55463400	Strong transcription	Lung	lung
43	chr2:55461600-55463600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:55461600-55463600	Strong transcription	Left Ventricle	heart
45	chr2:55461600-55463800	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr2:55461600-55464400	Strong transcription	Colonic Mucosa	Colon
47	chr2:55461600-55464400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr2:55461600-55464600	Strong transcription	Placenta	Placenta
49	chr2:55461600-55466600	Strong transcription	Fetal Intestine Large	intestine
50	chr2:55461600-55466600	Strong transcription	HSMMtube	muscle

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