Variant report

Variant	rs2296662
Chromosome Location	chr6:35744769-35744770
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	CTCF	chr6:35744680-35744830	BE2_C	brain:	n/a	n/a
2	ZBTB7A	chr6:35744227-35744787	K562	blood:	n/a	n/a
3	HA-E2F1	chr6:35744046-35744892	MCF-7	breast:	n/a	chr6:35744243-35744250
4	CTCF	chr6:35744620-35744770	HepG2	liver:	n/a	chr6:35744648-35744666 chr6:35744654-35744663 chr6:35744643-35744664
5	POLR2A	chr6:35744063-35744854	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr6:35744029-35745014	H1-hESC	embryonic stem cell:	n/a	chr6:35744323-35744334 chr6:35744322-35744335 chr6:35744324-35744333 chr6:35744324-35744333
7	CTCF	chr6:35744620-35744770	GM12866	blood:	n/a	chr6:35744648-35744666 chr6:35744654-35744663 chr6:35744643-35744664
8	MAX	chr6:35744083-35744857	MCF-7	breast:	n/a	chr6:35744323-35744334 chr6:35744322-35744335 chr6:35744324-35744333 chr6:35744324-35744333
9	TCF7L2	chr6:35744176-35744904	HCT-116	colon:	n/a	chr6:35744629-35744643
10	CTCF	chr6:35744640-35744790	GM12871	blood:	n/a	chr6:35744648-35744666 chr6:35744654-35744663 chr6:35744643-35744664
11	ZBTB7A	chr6:35744095-35744938	ECC-1	luminal epithelium:	n/a	n/a
12	RAD21	chr6:35744155-35744829	H1-hESC	embryonic stem cell:	n/a	chr6:35744646-35744665
13	TCF7L2	chr6:35744290-35744904	MCF-7	breast:	n/a	chr6:35744629-35744643
14	ZBTB7A	chr6:35744052-35745218	ECC-1	luminal epithelium:	n/a	n/a
15	E2F6	chr6:35743944-35745054	H1-hESC	embryonic stem cell:	n/a	chr6:35744243-35744250
16	TCF7L2	chr6:35744344-35744785	PANC-1	pancreas:	n/a	chr6:35744629-35744643
17	CTCF	chr6:35744620-35744770	HPAF	blood vessel:	n/a	chr6:35744648-35744666 chr6:35744654-35744663 chr6:35744643-35744664
18	MAZ	chr6:35744635-35744809	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:35744171-35744805	H1-hESC	embryonic stem cell:	n/a	n/a
20	NR2F2	chr6:35744114-35744920	MCF-7	breast:	n/a	n/a
21	POLR2A	chr6:35744114-35744808	H1-hESC	embryonic stem cell:	n/a	n/a
22	E2F6	chr6:35744037-35744939	H1-hESC	embryonic stem cell:	n/a	chr6:35744243-35744250
23	MAX	chr6:35744151-35744885	H1-hESC	embryonic stem cell:	n/a	chr6:35744323-35744334 chr6:35744322-35744335 chr6:35744324-35744333 chr6:35744324-35744333

No.	Distal block	Cell Line	Cell type
1	chr6:35742984..35745597-chr6:35763979..35765844,2	MCF-7	breast:
2	chr6:35732876..35736019-chr6:35742978..35745750,3	MCF-7	breast:
3	chr6:35743802..35745883-chr6:35771884..35774045,2	MCF-7	breast:
4	chr6:35744273..35746880-chr6:35754146..35757378,3	K562	blood:

Variant related genes	Relation type
CLPSL1	TF binding region
ENSG00000220734	Chromatin interaction
ENSG00000204140	Chromatin interaction
ENSG00000137392	Chromatin interaction
ENSG00000197753	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1107894	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs1326757	0.89[EUR][1000 genomes]
rs2478467	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs2766582	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2766583	0.84[EUR][1000 genomes]
rs2766584	0.84[EUR][1000 genomes]
rs2766585	0.84[EUR][1000 genomes]
rs2766587	0.84[EUR][1000 genomes]
rs2817064	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2817067	0.84[EUR][1000 genomes]
rs9357203	0.85[EUR][1000 genomes]
rs9470095	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv885802	chr6:35621781-35787417	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv885805	chr6:35685955-35779879	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv524941	chr6:35734051-35745655	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv525686	chr6:35734051-35750299	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv2762585	chr6:35734884-35747108	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv7891	chr6:35744190-35772539	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	esv1798998	chr6:35744609-35765951	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35744000-35744800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
2	chr6:35744000-35744800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:35744000-35744800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:35744000-35744800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:35744000-35744800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:35744000-35744800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr6:35744000-35744800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:35744000-35744800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:35744000-35744800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:35744000-35744800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:35744000-35744800	Active TSS	Duodenum Mucosa	Duodenum
12	chr6:35744000-35744800	Active TSS	A549	lung
13	chr6:35744000-35745000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:35744000-35745000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:35744000-35745000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:35744000-35745000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:35744000-35745000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:35744000-35745400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:35744200-35744800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:35744200-35744800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:35744200-35744800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:35744200-35744800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr6:35744200-35744800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:35744200-35744800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:35744200-35744800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:35744200-35744800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr6:35744200-35744800	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr6:35744200-35744800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
29	chr6:35744200-35744800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
30	chr6:35744200-35744800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:35744200-35744800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:35744200-35744800	Bivalent/Poised TSS	Aorta	Aorta
33	chr6:35744200-35744800	Enhancers	Liver	Liver
34	chr6:35744200-35744800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
35	chr6:35744200-35744800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
36	chr6:35744200-35744800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:35744200-35744800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
38	chr6:35744200-35744800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr6:35744200-35744800	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr6:35744200-35744800	Bivalent Enhancer	Fetal Thymus	thymus
41	chr6:35744200-35744800	Active TSS	Gastric	stomach
42	chr6:35744200-35744800	Active TSS	Rectal Smooth Muscle	rectum
43	chr6:35744200-35744800	Bivalent/Poised TSS	Thymus	Thymus
44	chr6:35744200-35744800	Enhancers	Spleen	Spleen
45	chr6:35744200-35744800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr6:35744200-35745000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:35744200-35745000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:35744200-35745000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:35744200-35745000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:35744200-35745000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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