Variant report

Variant	rs562026468
Chromosome Location	chr19:55954005-55954006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr19:55953915-55954328	K562	blood:	n/a	n/a
2	E2F6	chr19:55953720-55954295	K562	blood:	n/a	n/a
3	E2F6	chr19:55953356-55954255	K562	blood:	n/a	chr19:55953534-55953545
4	MAX	chr19:55953744-55954329	K562	blood:	n/a	n/a
5	MAX	chr19:55953765-55954127	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr19:55953776-55954032	MCF-7	breast:	n/a	n/a
7	SUZ12	chr19:55952383-55955792	NT2-D1	testis:	n/a	n/a
8	USF2	chr19:55953833-55954009	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr19:55953299-55954845	H1-hESC	embryonic stem cell:	n/a	chr19:55954296-55954308 chr19:55954363-55954372 chr19:55953534-55953545
10	HMGN3	chr19:55953903-55954214	K562	blood:	n/a	n/a
11	POLR2A	chr19:55953788-55954051	H1-neurons	neurons:	n/a	n/a
12	MAX	chr19:55953238-55954085	HCT-116	colon:	n/a	n/a
13	CTCF	chr19:55953865-55954044	MCF-7	breast:	n/a	n/a
14	MAX	chr19:55953772-55954184	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr19:55953849-55954073	MCF-7	breast:	n/a	n/a
16	CTCF	chr19:55953867-55954050	MCF-7	breast:	n/a	n/a
17	SIN3A	chr19:55953858-55954055	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr19:55953768-55954047	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr19:55952885-55954019	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr19:55953760-55954142	H1-neurons	neurons:	n/a	n/a
21	CTCF	chr19:55953985-55954005	K562	blood:	n/a	n/a
22	E2F6	chr19:55953793-55954361	H1-hESC	embryonic stem cell:	n/a	chr19:55954296-55954308
23	MAX	chr19:55953307-55954358	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr19:55953309-55954113	MCF-7	breast:	n/a	n/a
25	CTCF	chr19:55953916-55954015	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:55953996-55954046	HRCEpiC	kidney:	n/a
2	chr19:55953996-55954046	SK-N-SH_RA	brain:	n/a
3	chr19:55953996-55954046	NHDF-neo	bronchial:	n/a
4	chr19:55953996-55954046	GM12878	blood:	n/a
5	chr19:55953996-55954046	ProgFib	skin:	n/a
6	chr19:55953996-55954046	GM06990	blood:	n/a
7	chr19:55953996-55954046	SK-N-SH	brain:	n/a
8	chr19:55953996-55954046	PANC-1	pancreas:	n/a
9	chr19:55953996-55954046	Hela-S3	cervix:	n/a
10	chr19:55953996-55954046	NB4	blood:	n/a
11	chr19:55953996-55954046	AG04450	lung:	fetal
12	chr19:55953996-55954046	HCT-116	colon:	n/a
13	chr19:55953996-55954046	K562	blood:	n/a
14	chr19:55953996-55954046	U87	brain:	n/a
15	chr19:55953996-55954046	HUVEC	blood vessel:	n/a
16	chr19:55953996-55954046	PFSK-1	brain:	n/a
17	chr19:55953996-55954046	HRE	kidney:	n/a
18	chr19:55953996-55954046	NHBE	bronchial:	n/a
19	chr19:55953996-55954046	LNCaP	prostate:	n/a
20	chr19:55953996-55954046	ECC-1	luminal epithelium:	n/a
21	chr19:55953996-55954046	ovcar-3	ovarian:	n/a
22	chr19:55953996-55954046	NH-A	brain:	n/a
23	chr19:55953996-55954046	GM19239	blood:	n/a
24	chr19:55953996-55954046	IMR90	lung:	fetal
25	chr19:55953996-55954046	HEEpiC	esophagus:	n/a
26	chr19:55953996-55954046	HL-60	blood:	n/a
27	chr19:55953996-55954046	SAEC	small airway:	n/a
28	chr19:55953996-55954046	HMEC	breast:	n/a
29	chr19:55953996-55954046	RPTEC	kidney:	n/a
30	chr19:55953996-55954046	GM12892	blood:	n/a
31	chr19:55953996-55954046	AG09319	gingival:	n/a
32	chr19:55953996-55954046	HEK293	kidney:	embryo
33	chr19:55953996-55954046	HIPEpiC	eye:	n/a
34	chr19:55953996-55954046	Caco-2	colon:	n/a
35	chr19:55953996-55954046	BE2_C	brain:	n/a
36	chr19:55953996-55954046	PrEC	prostate:	n/a
37	chr19:55953996-55954046	HNPCEpiC	eye:	n/a
38	chr19:55953996-55954046	SK-N-MC	brain:	n/a
39	chr19:55953996-55954046	A549	lung:	n/a
40	chr19:55953996-55954046	CMK	blood:	n/a
41	chr19:55953996-55954046	AoSMC	blood vessel:	n/a
42	chr19:55953996-55954046	HRPEpiC	eye:	n/a
43	chr19:55953996-55954046	AG10803	skin:	n/a
44	chr19:55953996-55954046	AG09309	skin:	n/a
45	chr19:55953996-55954046	MCF-7	breast:	n/a
46	chr19:55953996-55954046	MCF10A-Er-Src	breast:	n/a
47	chr19:55953996-55954046	H1-hESC	embryonic stem cell:	embryo
48	chr19:55953996-55954046	HCM	heart:	n/a
49	chr19:55953996-55954046	AG04449	skin:	fetal
50	chr19:55953996-55954046	Hepatocyte	liver:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55897252..55900237-chr19:55952546..55954535,2	K562	blood:
2	chr19:55949680..55954432-chr19:55969839..55974899,6	K562	blood:
3	chr19:55917609..55921205-chr19:55953986..55957164,3	MCF-7	breast:
4	chr19:55953960..55955842-chr19:55970927..55973653,2	MCF-7	breast:
5	chr19:55917160..55920807-chr19:55952217..55954554,6	K562	blood:
6	chr19:55896562..55898629-chr19:55953119..55955892,2	MCF-7	breast:
7	chr19:55917160..55921382-chr19:55952217..55958073,12	K562	blood:
8	chr19:55766019..55768173-chr19:55952216..55954290,2	K562	blood:
9	chr19:55910844..55913006-chr19:55952542..55954951,2	K562	blood:
10	chr19:55789771..55793296-chr19:55950803..55954133,4	K562	blood:

No data

Variant related genes	Relation type
SHISA7	TF binding region
SHISA7	CpG island
ENSG00000267093	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000063241	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
2	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
4	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv912477	chr19:55936376-55972950	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv912478	chr19:55936376-56045522	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
7	nsv912479	chr19:55942456-55969746	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	esv3376613	chr19:55952665-55955513	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
9	esv3422614	chr19:55952890-55955638	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55951600-55955200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr19:55951600-55955200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr19:55951800-55954800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:55951800-55955000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr19:55952000-55954600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr19:55952000-55954800	Bivalent Enhancer	Fetal Stomach	stomach
7	chr19:55952000-55955200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
8	chr19:55952200-55955400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:55952400-55954200	Weak transcription	Pancreas	Pancrea
10	chr19:55952600-55954200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:55952600-55954800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:55952800-55955000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:55952800-55955600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
14	chr19:55953000-55954400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
15	chr19:55953200-55954400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
16	chr19:55953200-55954600	Bivalent Enhancer	Lung	lung
17	chr19:55953400-55954200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:55953400-55954200	Enhancers	Right Atrium	heart
19	chr19:55953400-55954400	Weak transcription	Brain Substantia Nigra	brain
20	chr19:55953400-55954400	Bivalent Enhancer	Right Ventricle	heart
21	chr19:55953400-55954800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:55953400-55955000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr19:55953400-55955000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr19:55953400-55955200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
25	chr19:55953400-55956400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr19:55953600-55954200	Flanking Bivalent TSS/Enh	Thymus	Thymus
27	chr19:55953600-55954400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:55953600-55954400	Active TSS	K562	blood
29	chr19:55953600-55954600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
30	chr19:55953600-55954600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:55953600-55954600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:55953600-55954800	Enhancers	Primary hematopoietic stem cells	blood
33	chr19:55953600-55954800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr19:55953600-55955000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr19:55953600-55955000	Active TSS	Brain Anterior Caudate	brain
36	chr19:55953600-55955000	Active TSS	Brain Cingulate Gyrus	brain
37	chr19:55953600-55955000	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr19:55953600-55955200	Bivalent Enhancer	Spleen	Spleen
39	chr19:55953800-55954400	Active TSS	Brain Angular Gyrus	brain
40	chr19:55954000-55954400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:55954000-55954400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
42	chr19:55954000-55954600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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