Variant report

Variant	rs559590025
Chromosome Location	chr1:156339344-156339345
allele	G/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	TAF1	chr1:156338638-156339401	HepG2	liver:	n/a	n/a
2	HEY1	chr1:156338560-156339508	HepG2	liver:	n/a	chr1:156338975-156338990
3	POLR2A	chr1:156338685-156339828	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:156336907-156344214	HepG2	liver:	n/a	n/a
5	MBD4	chr1:156339265-156339896	HepG2	liver:	n/a	n/a
6	MAX	chr1:156338583-156339371	MCF-7	breast:	n/a	chr1:156338955-156338965 chr1:156338925-156338935
7	GATA3	chr1:156338575-156339416	MCF-7	breast:	n/a	chr1:156338736-156338745
8	ZEB1	chr1:156336577-156339970	HepG2	liver:	n/a	chr1:156338920-156338927
9	POLR2A	chr1:156338600-156339892	HepG2	liver:	n/a	n/a
10	HA-E2F1	chr1:156338776-156339383	MCF-7	breast:	n/a	chr1:156338980-156338990 chr1:156339245-156339257
11	POLR2A	chr1:156338698-156339421	H1-hESC	embryonic stem cell:	n/a	n/a
12	HEY1	chr1:156338531-156339877	HepG2	liver:	n/a	chr1:156338975-156338990

No.	Distal block	Cell Line	Cell type
1	chr1:156337757..156339382-chr1:156424916..156426755,2	MCF-7	breast:
2	chr1:156335306..156343282-chr1:156347773..156352892,8	MCF-7	breast:
3	chr1:156304937..156307794-chr1:156336669..156339422,4	MCF-7	breast:
4	chr1:156305358..156309501-chr1:156336177..156340436,7	MCF-7	breast:

Variant related genes	Relation type
CCT3	TF binding region
ENSG00000236947	Chromatin interaction
ENSG00000132677	Chromatin interaction
ENSG00000163467	Chromatin interaction
ENSG00000163468	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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv915822	chr1:156226286-156651655	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases
4	nsv872471	chr1:156287360-156356480	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv470742	chr1:156335111-156354367	Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv1793632	chr1:156338992-156366178	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156338200-156341400	Weak transcription	Hela-S3	cervix
2	chr1:156338600-156339400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:156338600-156339400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:156338600-156339400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:156338600-156339400	Active TSS	Duodenum Mucosa	Duodenum
6	chr1:156338600-156339400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
7	chr1:156338600-156339600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:156338600-156339600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:156338600-156339600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:156338600-156339600	Flanking Active TSS	Ovary	ovary
11	chr1:156338600-156339600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
12	chr1:156338600-156339800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:156338600-156339800	Flanking Active TSS	Liver	Liver
14	chr1:156338800-156339400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:156338800-156339400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:156338800-156339400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:156338800-156339400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:156338800-156339400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
19	chr1:156338800-156339400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
20	chr1:156338800-156339400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
21	chr1:156338800-156339400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
22	chr1:156338800-156339400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:156338800-156339400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr1:156338800-156339400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:156338800-156339400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:156338800-156339400	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr1:156338800-156339400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
28	chr1:156338800-156339400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:156338800-156339400	Active TSS	Brain Substantia Nigra	brain
30	chr1:156338800-156339400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
31	chr1:156338800-156339400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
32	chr1:156338800-156339400	Bivalent Enhancer	Fetal Thymus	thymus
33	chr1:156338800-156339400	Flanking Active TSS	Lung	lung
34	chr1:156338800-156339400	Bivalent/Poised TSS	Psoas Muscle	Psoas
35	chr1:156338800-156339400	Active TSS	Right Atrium	heart
36	chr1:156338800-156339400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
37	chr1:156338800-156339400	Active TSS	A549	lung
38	chr1:156338800-156339400	Bivalent/Poised TSS	HSMM	muscle
39	chr1:156338800-156339400	Flanking Bivalent TSS/Enh	NH-A	brain
40	chr1:156338800-156339600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:156338800-156339600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:156338800-156339600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:156338800-156339600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:156338800-156339600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
45	chr1:156338800-156339600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr1:156338800-156339600	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:156338800-156339600	Bivalent Enhancer	Fetal Muscle Leg	muscle
48	chr1:156338800-156339600	Flanking Active TSS	HMEC	breast
49	chr1:156338800-156339800	Flanking Active TSS	Spleen	Spleen
50	chr1:156338800-156339800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

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