Variant report

Variant	rs577940408
Chromosome Location	chr6:12749716-12749717
allele	-/TTT
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	chr6:12749216-12749719	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF2	chr6:12749240-12749753	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr6:12748563-12750726	H1-hESC	embryonic stem cell:	n/a	n/a
4	YY1	chr6:12749448-12749745	H1-hESC	embryonic stem cell:	n/a	n/a
5	EP300	chr6:12749370-12749756	H1-hESC	embryonic stem cell:	n/a	chr6:12749523-12749539
6	SP4	chr6:12749411-12749753	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUND	chr6:12749403-12749727	H1-hESC	embryonic stem cell:	n/a	chr6:12749532-12749541
8	E2F6	chr6:12749217-12749731	H1-hESC	embryonic stem cell:	n/a	chr6:12749603-12749613 chr6:12749428-12749436 chr6:12749428-12749438 chr6:12749430-12749445 chr6:12749353-12749362 chr6:12749429-12749436 chr6:12749429-12749437 chr6:12749428-12749439 chr6:12749429-12749440 chr6:12749533-12749542 chr6:12749429-12749437
9	EGR1	chr6:12749385-12749896	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr6:12748447-12750926	SK-N-SH	brain:	n/a	n/a
11	ATF2	chr6:12749410-12749743	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTBP2	chr6:12748829-12750689	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr6:12749448-12749750	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP1	chr6:12749233-12749748	H1-hESC	embryonic stem cell:	n/a	chr6:12749533-12749543 chr6:12749534-12749543 chr6:12749529-12749543 chr6:12749533-12749542 chr6:12749532-12749544
15	MYC	chr6:12749500-12749734	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3AK20	chr6:12749458-12749766	H1-hESC	embryonic stem cell:	n/a	n/a
17	SP1	chr6:12749277-12749874	H1-hESC	embryonic stem cell:	n/a	chr6:12749533-12749543 chr6:12749534-12749543 chr6:12749529-12749543 chr6:12749533-12749542 chr6:12749532-12749544
18	JUND	chr6:12749421-12749723	H1-hESC	embryonic stem cell:	n/a	chr6:12749532-12749541
19	GTF2F1	chr6:12749492-12749771	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr6:12749145-12750227	H1-hESC	embryonic stem cell:	n/a	chr6:12750203-12750217
21	JUND	chr6:12749416-12749717	H1-hESC	embryonic stem cell:	n/a	chr6:12749532-12749541
22	TBP	chr6:12749262-12749960	H1-hESC	embryonic stem cell:	n/a	n/a
23	RFX5	chr6:12749468-12749768	H1-hESC	embryonic stem cell:	n/a	n/a
24	JUN	chr6:12749457-12749724	H1-hESC	embryonic stem cell:	n/a	chr6:12749532-12749541
25	MAX	chr6:12749227-12750659	H1-hESC	embryonic stem cell:	n/a	chr6:12750472-12750482
26	CHD2	chr6:12749451-12749812	H1-hESC	embryonic stem cell:	n/a	chr6:12749529-12749539
27	POLR2A	chr6:12749194-12750748	H1-neurons	neurons:	n/a	n/a
28	MAFK	chr6:12749276-12749733	H1-hESC	embryonic stem cell:	n/a	chr6:12749444-12749459 chr6:12749447-12749463 chr6:12749445-12749465 chr6:12749448-12749462
29	EGR1	chr6:12749338-12749794	H1-hESC	embryonic stem cell:	n/a	chr6:12749353-12749363
30	TCF12	chr6:12749537-12749744	H1-hESC	embryonic stem cell:	n/a	n/a
31	REST	chr6:12748947-12751024	H1-neurons	neurons:	n/a	chr6:12750584-12750604 chr6:12750905-12750923 chr6:12750584-12750604 chr6:12750914-12750932
32	ZNF143	chr6:12749122-12750239	H1-hESC	embryonic stem cell:	n/a	chr6:12749353-12749363
33	RAD21	chr6:12749325-12749999	H1-hESC	embryonic stem cell:	n/a	chr6:12749436-12749448

Variant related genes	Relation type
ENSG00000223291	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3361165	chr6:12748791-12751339	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
4	esv3432117	chr6:12748916-12751314	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12748800-12750400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:12748800-12750600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:12748800-12750600	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:12748800-12750600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:12748800-12750600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:12748800-12751000	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:12748800-12752600	Active TSS	Fetal Brain Female	brain
8	chr6:12749000-12750400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:12749000-12750400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:12749000-12750600	Active TSS	HSMM	muscle
11	chr6:12749000-12750800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:12749000-12751000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:12749000-12751000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:12749200-12749800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:12749200-12749800	Enhancers	Right Atrium	heart
16	chr6:12749200-12750000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:12749200-12750200	Enhancers	Gastric	stomach
18	chr6:12749200-12750200	Enhancers	Pancreas	Pancrea
19	chr6:12749200-12750400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:12749200-12750400	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr6:12749200-12750400	Enhancers	Fetal Brain Male	brain
22	chr6:12749200-12750600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:12749200-12750600	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:12749200-12750600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
25	chr6:12749200-12750600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
26	chr6:12749200-12750600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
27	chr6:12749200-12750600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:12749200-12750600	Bivalent Enhancer	Left Ventricle	heart
29	chr6:12749200-12751000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:12749400-12749800	Active TSS	Brain Germinal Matrix	brain
31	chr6:12749400-12749800	Bivalent Enhancer	Fetal Stomach	stomach
32	chr6:12749400-12749800	Enhancers	Spleen	Spleen
33	chr6:12749400-12750000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:12749400-12750000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
35	chr6:12749400-12750400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:12749400-12750600	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr6:12749400-12750600	Active TSS	HSMMtube	muscle
38	chr6:12749400-12750800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:12749600-12749800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
40	chr6:12749600-12749800	Bivalent Enhancer	Brain Hippocampus Middle	brain
41	chr6:12749600-12749800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
42	chr6:12749600-12749800	Bivalent/Poised TSS	Right Ventricle	heart
43	chr6:12749600-12750000	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
44	chr6:12749600-12750000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:12749600-12750200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:12749600-12750200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:12749600-12750200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:12749600-12750400	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:12749600-12750400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
50	chr6:12749600-12750600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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