Variant report

Variant	rs538878371
Chromosome Location	chr12:56117944-56117945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:70)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:70 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56116371-56118897	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:56116320-56119253	ProgFib	skin:	n/a	n/a
3	BCL3	chr12:56117805-56118681	A549	lung:	n/a	n/a
4	PML	chr12:56117788-56118988	K562	blood:	n/a	n/a
5	POLR2A	chr12:56113532-56124497	U87	brain:	n/a	n/a
6	PML	chr12:56117944-56118934	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:56117447-56118801	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:56116248-56119994	A549	lung:	n/a	n/a
9	POLR2A	chr12:56117422-56118720	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr12:56117328-56118733	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:56117833-56118332	A549	lung:	n/a	n/a
12	MTA3	chr12:56116495-56118107	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:56117488-56118738	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:56117570-56118408	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:56117444-56118402	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr12:56117518-56118811	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:56116602-56119733	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:56117853-56118330	A549	lung:	n/a	n/a
19	POLR2A	chr12:56117769-56118882	PBDE	blood:	n/a	n/a
20	CTCF	chr12:56117940-56119080	A549	lung:	n/a	n/a
21	POLR2A	chr12:56117426-56118796	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr12:56117452-56119193	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr12:56117404-56119110	K562	blood:	n/a	n/a
24	POLR2A	chr12:56117810-56118347	GM12891	blood:	n/a	n/a
25	POLR2A	chr12:56117434-56118991	K562	blood:	n/a	n/a
26	POLR2A	chr12:56117464-56117966	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr12:56117399-56118783	GM12891	blood:	n/a	n/a
28	POLR2A	chr12:56117595-56119017	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:56117603-56119103	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:56117813-56118592	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr12:56117497-56119163	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:56113762-56120156	U87	brain:	n/a	n/a
33	POLR2A	chr12:56116536-56118003	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr12:56117869-56118328	A549	lung:	n/a	n/a
35	POLR2A	chr12:56116741-56119954	K562	blood:	n/a	n/a
36	POLR2A	chr12:56117502-56119048	MCF-7	breast:	n/a	n/a
37	MYC	chr12:56117912-56118045	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:56116242-56120054	K562	blood:	n/a	n/a
39	POLR2A	chr12:56117619-56118335	A549	lung:	n/a	n/a
40	TEAD4	chr12:56117870-56119028	K562	blood:	n/a	n/a
41	POLR2A	chr12:56117428-56119056	GM12892	blood:	n/a	n/a
42	POLR2A	chr12:56116315-56119345	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:56116644-56119510	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:56116187-56118999	K562	blood:	n/a	n/a
45	POLR2A	chr12:56117564-56118322	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:56117669-56118978	GM12891	blood:	n/a	n/a
47	POLR2A	chr12:56117901-56118627	GM12892	blood:	n/a	n/a
48	POLR2A	chr12:56116133-56119487	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr12:56117892-56119069	GM12891	blood:	n/a	n/a
50	POLR2A	chr12:56116546-56120067	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:56115949..56118195-chr12:56224037..56226803,2	MCF-7	breast:
2	chr12:56117197..56125255-chr12:56135299..56142277,21	K562	blood:
3	chr12:56037529..56040108-chr12:56117252..56119317,2	K562	blood:
4	chr12:56088490..56090282-chr12:56117395..56118988,2	MCF-7	breast:
5	chr12:56075054..56077566-chr12:56115620..56119645,3	MCF-7	breast:
6	chr12:56117825..56119634-chr17:57178406..57181247,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258056	TF binding region
ENSG00000182796	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000170439	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000135392	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv559005	chr12:56117570-56120934	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	20 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	chr12:56111200-56120400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:56111600-56118400	Strong transcription	Thymus	Thymus
3	chr12:56112200-56118000	Weak transcription	Fetal Lung	lung
4	chr12:56112400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:56112600-56118200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:56112600-56118800	Weak transcription	Small Intestine	intestine
7	chr12:56112800-56120800	Weak transcription	Fetal Brain Male	brain
8	chr12:56112800-56121000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:56113200-56118000	Weak transcription	Ovary	ovary
10	chr12:56113200-56118600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:56113200-56120000	Strong transcription	Brain Germinal Matrix	brain
12	chr12:56113200-56120800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:56114200-56118600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:56114400-56118000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:56114400-56118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:56114400-56121000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:56114600-56118000	Weak transcription	Fetal Kidney	kidney
18	chr12:56114800-56118200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:56115000-56118600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:56115000-56118600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:56115000-56120400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:56115200-56118200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:56115400-56118000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:56115400-56118000	Weak transcription	Brain Angular Gyrus	brain
25	chr12:56115400-56118400	Weak transcription	K562	blood
26	chr12:56115400-56118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:56115400-56120400	Genic enhancers	Fetal Intestine Large	intestine
28	chr12:56115400-56120400	Strong transcription	Fetal Stomach	stomach
29	chr12:56115400-56120600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:56115400-56121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:56115400-56121200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:56115600-56118000	Weak transcription	Hela-S3	cervix
33	chr12:56115600-56120400	Strong transcription	Lung	lung
34	chr12:56115600-56120600	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr12:56115600-56120800	Genic enhancers	Fetal Muscle Leg	muscle
36	chr12:56116000-56120600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:56116200-56118600	Strong transcription	NHEK	skin
38	chr12:56116200-56120400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:56116400-56120400	Genic enhancers	Fetal Intestine Small	intestine
40	chr12:56116600-56118200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:56116600-56118400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr12:56116600-56118600	Strong transcription	Brain Anterior Caudate	brain
43	chr12:56116600-56119400	Genic enhancers	Right Ventricle	heart
44	chr12:56116600-56119600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:56116600-56120200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:56116600-56120400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:56116600-56120400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:56116600-56120400	Genic enhancers	Adipose Nuclei	Adipose
49	chr12:56116600-56120400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
50	chr12:56116600-56120600	Genic enhancers	Rectal Mucosa Donor 29	rectum

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