Variant report

Variant	rs377223272
Chromosome Location	chr2:55462111-55462112
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:49)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:49 , 50 per page) page: 1

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	chr2:55458959-55464692	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:55458747-55464848	U87	brain:	n/a	n/a
6	POLR2A	chr2:55458731-55465585	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:55458589-55462559	HCT-116	colon:	n/a	n/a
8	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr2:55458760-55464736	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:55461373-55464681	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:55459164-55464717	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:55458775-55464779	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:55458974-55464629	K562	blood:	n/a	n/a
15	POLR2A	chr2:55458800-55464614	K562	blood:	n/a	n/a
16	POLR2A	chr2:55458988-55464662	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:55461692-55462150	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr2:55461469-55464573	K562	blood:	n/a	n/a
19	POLR2A	chr2:55458860-55465354	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr2:55458989-55464724	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr2:55458966-55464603	GM12892	blood:	n/a	n/a
22	POLR2A	chr2:55459024-55464715	GM18505	blood:	n/a	n/a
23	POLR2A	chr2:55458733-55465490	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:55461687-55462658	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr2:55458865-55465521	MCF-7	breast:	n/a	n/a
26	POLR2A	chr2:55460323-55464639	A549	lung:	n/a	n/a
27	POLR2A	chr2:55458817-55464677	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:55461565-55464760	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr2:55458685-55467019	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr2:55459009-55464639	GM12892	blood:	n/a	n/a
31	POLR2A	chr2:55459696-55465435	K562	blood:	n/a	n/a
32	POLR2A	chr2:55458747-55464854	U87	brain:	n/a	n/a
33	BCL3	chr2:55461606-55462520	A549	lung:	n/a	n/a
34	POLR2A	chr2:55461332-55462156	GM12891	blood:	n/a	n/a
35	POLR2A	chr2:55461740-55462209	GM12891	blood:	n/a	n/a
36	POLR2A	chr2:55458947-55464599	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr2:55461354-55464525	GM12891	blood:	n/a	n/a
38	POLR2A	chr2:55461854-55463961	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr2:55458451-55467274	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr2:55458733-55464641	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:55461538-55464657	GM12892	blood:	n/a	n/a
42	POLR2A	chr2:55461478-55464741	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr2:55462046-55462615	K562	blood:	n/a	n/a
44	POLR2A	chr2:55458884-55465602	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr2:55461395-55462255	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:55458900-55464628	GM12892	blood:	n/a	n/a
47	POLR2A	chr2:55461626-55464653	HepG2	liver:	n/a	n/a
48	POLR2A	chr2:55460880-55464562	K562	blood:	n/a	n/a
49	HEY1	chr2:55458747-55462183	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
2	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
3	chr17:57919487..57921628-chr2:55460501..55462131,2	MCF-7	breast:
4	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:
5	chr2:55461063..55464036-chr2:55678930..55681673,2	MCF-7	breast:
6	chr2:55313997..55316994-chr2:55461231..55462844,2	K562	blood:

No data

Variant related genes	Relation type
CLHC1	TF binding region
ENSG00000085760	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000138041	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	chr2:55458600-55462200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:55460000-55462400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
3	chr2:55460000-55463000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
4	chr2:55460000-55463400	Transcr. at gene 5' and 3'	K562	blood
5	chr2:55460200-55462200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:55460200-55462600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr2:55460200-55463000	Transcr. at gene 5' and 3'	A549	lung
8	chr2:55460400-55462400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
9	chr2:55460400-55462400	Transcr. at gene 5' and 3'	Hela-S3	cervix
10	chr2:55460400-55462600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
11	chr2:55460400-55462600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:55460400-55463000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:55460600-55462200	Transcr. at gene 5' and 3'	NH-A	brain
14	chr2:55460600-55462400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
15	chr2:55460600-55462600	Weak transcription	Aorta	Aorta
16	chr2:55460600-55463400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:55460600-55463800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
18	chr2:55460800-55462200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:55460800-55462600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
20	chr2:55460800-55462600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
21	chr2:55461000-55462200	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr2:55461000-55462200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:55461000-55462400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:55461000-55462400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr2:55461000-55462400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:55461000-55462400	Genic enhancers	Brain Hippocampus Middle	brain
27	chr2:55461000-55462600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:55461000-55462800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:55461000-55463000	Genic enhancers	Brain Germinal Matrix	brain
30	chr2:55461000-55463000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr2:55461000-55464600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:55461000-55470200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:55461200-55462400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:55461200-55462400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:55461200-55462400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:55461200-55462400	Genic enhancers	Brain Cingulate Gyrus	brain
37	chr2:55461200-55462400	Genic enhancers	Rectal Mucosa Donor 29	rectum
38	chr2:55461200-55462600	Genic enhancers	NHDF-Ad	bronchial
39	chr2:55461200-55462800	Weak transcription	Pancreas	Pancrea
40	chr2:55461200-55463000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:55461200-55463000	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr2:55461200-55463200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr2:55461200-55463200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:55461200-55463600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr2:55461200-55463600	Strong transcription	Thymus	Thymus
46	chr2:55461200-55464600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:55461200-55464800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:55461400-55462200	Genic enhancers	Small Intestine	intestine
49	chr2:55461400-55462400	Strong transcription	Brain Angular Gyrus	brain
50	chr2:55461400-55463000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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