Variant report

Variant	rs28742061
Chromosome Location	chr1:224805209-224805210
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	MAX	chr1:224804476-224805789	H1-hESC	embryonic stem cell:	n/a	chr1:224805041-224805050
2	MAX	chr1:224803269-224805331	H1-hESC	embryonic stem cell:	n/a	chr1:224803735-224803742 chr1:224805041-224805050
3	E2F6	chr1:224803256-224805378	H1-hESC	embryonic stem cell:	n/a	chr1:224803938-224803952 chr1:224803665-224803675 chr1:224804409-224804424 chr1:224805253-224805265
4	E2F6	chr1:224803117-224805791	H1-hESC	embryonic stem cell:	n/a	chr1:224803938-224803952 chr1:224803665-224803675 chr1:224804409-224804424 chr1:224805253-224805265
5	SUZ12	chr1:224804113-224806096	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTBP2	chr1:224803557-224806095	H1-hESC	embryonic stem cell:	n/a	n/a
7	SUZ12	chr1:224803428-224806408	NT2-D1	testis:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224760255..224762194-chr1:224803067..224805853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233384	TF binding region
ENSG00000229991	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10082162	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16849891	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58166431	1.00[EUR][1000 genomes]
rs6689431	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224803200-224805800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr1:224803200-224805800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:224803200-224806400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:224803200-224806400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
5	chr1:224803200-224807000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:224803200-224807000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:224803200-224807200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:224803200-224807400	Active TSS	NHDF-Ad	bronchial
9	chr1:224803400-224805400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:224803400-224805800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:224803400-224805800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:224803400-224806800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
13	chr1:224803600-224805400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:224803600-224805600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:224803600-224805800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:224803600-224805800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:224803600-224806200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr1:224803600-224806400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:224803800-224805400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:224803800-224805400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:224803800-224805800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:224803800-224806200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:224803800-224806200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:224803800-224807800	Active TSS	NH-A	brain
25	chr1:224804000-224805400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:224804200-224805400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
27	chr1:224804200-224805400	Flanking Bivalent TSS/Enh	Dnd41	blood
28	chr1:224804200-224805600	Bivalent Enhancer	Liver	Liver
29	chr1:224804200-224806000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:224804200-224806200	Bivalent/Poised TSS	Fetal Kidney	kidney
31	chr1:224804400-224805400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr1:224804400-224805800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:224804400-224806000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr1:224804400-224806000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:224804400-224806400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:224804600-224805800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:224804600-224805800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:224804600-224805800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr1:224804600-224806600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
40	chr1:224804800-224805600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:224804800-224805600	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr1:224804800-224805600	Active TSS	NHLF	lung
43	chr1:224804800-224805800	Flanking Active TSS	Pancreas	Pancrea
44	chr1:224804800-224805800	Flanking Bivalent TSS/Enh	HMEC	breast
45	chr1:224804800-224806000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:224804800-224806000	Bivalent Enhancer	Esophagus	oesophagus
47	chr1:224804800-224806200	Bivalent Enhancer	Fetal Thymus	thymus
48	chr1:224804800-224807000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
49	chr1:224805000-224805400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
50	chr1:224805000-224805400	Bivalent Enhancer	Right Ventricle	heart

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