Variant report

Variant	rs539039997
Chromosome Location	chr1:78418589-78418590
allele	C/G
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	chr1:78414812-78418855	K562	blood:	n/a	n/a
2	POLR2A	chr1:78418478-78418824	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:78418070-78418912	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:78418367-78419029	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:78418455-78418836	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:78416640-78419183	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:78418066-78419141	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:78418559-78418975	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78416931..78420284-chr1:78442371..78445567,3	MCF-7	breast:

Variant related genes	Relation type
FUBP1	TF binding region
ENSG00000137960	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000162613	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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 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	chr1:78372800-78418600	Weak transcription	Pancreas	Pancrea
2	chr1:78383600-78418600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:78392200-78420400	Strong transcription	HSMM	muscle
4	chr1:78393000-78418600	Weak transcription	Lung	lung
5	chr1:78396800-78419600	Weak transcription	Ovary	ovary
6	chr1:78397800-78418600	Weak transcription	Spleen	Spleen
7	chr1:78403000-78418800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:78405000-78418600	Weak transcription	Aorta	Aorta
9	chr1:78405800-78432200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
11	chr1:78406000-78420200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:78406000-78426600	Weak transcription	Fetal Heart	heart
13	chr1:78406000-78436200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:78406600-78436200	Strong transcription	Liver	Liver
15	chr1:78406600-78440600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:78406800-78436400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:78407000-78434400	Strong transcription	Dnd41	blood
18	chr1:78407000-78437200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:78407400-78427600	Strong transcription	Fetal Intestine Large	intestine
20	chr1:78407400-78432800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:78407400-78436600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr1:78407400-78437600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:78407400-78437800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:78407600-78435400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:78407600-78435600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:78407600-78437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:78407800-78420400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:78407800-78435400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:78407800-78436800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:78407800-78437200	Strong transcription	Placenta	Placenta
31	chr1:78408000-78437600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:78408200-78434200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:78408400-78436400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:78408400-78439600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:78408600-78437000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:78409200-78418600	Weak transcription	Right Ventricle	heart
37	chr1:78409600-78432000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:78409600-78432200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:78409600-78437200	Strong transcription	Hela-S3	cervix
40	chr1:78410000-78433800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:78410600-78427400	Strong transcription	HepG2	liver
42	chr1:78411200-78418600	Weak transcription	Esophagus	oesophagus
43	chr1:78411400-78420800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr1:78411800-78421000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:78411800-78438200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:78412400-78434800	Strong transcription	Fetal Lung	lung
47	chr1:78412800-78434800	Strong transcription	Fetal Brain Female	brain
48	chr1:78413000-78423000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:78413000-78432600	Strong transcription	Primary T cells from cord blood	blood
50	chr1:78413400-78419600	Weak transcription	Brain Angular Gyrus	brain

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