Variant report

Variant	rs558934489
Chromosome Location	chr19:56149998-56149999
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	POLR2A	chr19:56149674-56150180	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:56149671-56150178	K562	blood:	n/a	n/a
3	POLR2A	chr19:56149778-56157300	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:56148727-56151140	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr19:56146066-56155822	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr19:56149442-56155618	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:56149709-56150010	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:56149741-56156388	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56109287..56112853-chr19:56149861..56154883,7	MCF-7	breast:
2	chr19:56135345..56138507-chr19:56147845..56151809,4	K562	blood:

Variant related genes	Relation type
ZNF580	TF binding region
CCDC106	TF binding region
ZNF581	TF binding region
ENSG00000179943	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000179922	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	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS 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 target site	67 gene(s)	inside rSNPs	diseases
5	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
6	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
9	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56147600-56150400	Weak transcription	Fetal Brain Female	brain
2	chr19:56147800-56150400	Strong transcription	Fetal Intestine Small	intestine
3	chr19:56147800-56151400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:56147800-56151400	Enhancers	Liver	Liver
5	chr19:56147800-56151400	Enhancers	Brain Substantia Nigra	brain
6	chr19:56147800-56151600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:56147800-56151600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:56147800-56151600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:56147800-56151600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:56147800-56151600	Weak transcription	Fetal Heart	heart
11	chr19:56147800-56151600	Enhancers	Pancreas	Pancrea
12	chr19:56147800-56151800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:56147800-56151800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr19:56148000-56150400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:56148000-56150400	Weak transcription	Fetal Brain Male	brain
16	chr19:56148000-56150600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:56148000-56150800	Weak transcription	Fetal Kidney	kidney
18	chr19:56148000-56151400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr19:56148200-56150000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:56148200-56150000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr19:56148200-56150400	Strong transcription	Fetal Stomach	stomach
22	chr19:56148200-56150400	Weak transcription	NHDF-Ad	bronchial
23	chr19:56148200-56150600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:56148200-56150600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:56148200-56150600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:56148200-56151000	Weak transcription	Stomach Mucosa	stomach
27	chr19:56148200-56151200	Weak transcription	Small Intestine	intestine
28	chr19:56148200-56151200	Weak transcription	HUVEC	blood vessel
29	chr19:56148200-56151400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:56148200-56151400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:56148200-56151400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:56148200-56151400	Weak transcription	HMEC	breast
33	chr19:56148200-56151400	Weak transcription	HSMM	muscle
34	chr19:56148200-56151400	Weak transcription	HSMMtube	muscle
35	chr19:56148200-56151400	Weak transcription	NHEK	skin
36	chr19:56148200-56151600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:56148200-56151600	Enhancers	Adipose Nuclei	Adipose
38	chr19:56148200-56151800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:56148200-56151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:56148400-56150000	Weak transcription	K562	blood
41	chr19:56148400-56150400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:56148400-56150400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr19:56148400-56150600	Weak transcription	Right Atrium	heart
44	chr19:56148400-56150600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:56148400-56151200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:56148400-56151200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr19:56148400-56151200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr19:56148400-56151200	Weak transcription	Colonic Mucosa	Colon
49	chr19:56148400-56151200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:56148400-56151200	Weak transcription	Monocytes-CD14+_RO01746	blood

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