Variant report

Variant	rs562367441
Chromosome Location	chr10:98590562-98590563
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	CTCF	chr10:98590369-98590635	K562	blood:	n/a	chr10:98590477-98590490
2	CTCF	chr10:98590344-98590669	ECC-1	luminal epithelium:	n/a	chr10:98590477-98590490
3	CTCF	chr10:98590330-98590638	T-47D	breast:	n/a	chr10:98590477-98590490
4	CTCF	chr10:98590172-98590774	HCT-116	colon:	n/a	chr10:98590477-98590490
5	CTCF	chr10:98590420-98590570	GM12872	blood:	n/a	chr10:98590477-98590490
6	CTCF	chr10:98590211-98590648	MCF-7	breast:	n/a	chr10:98590477-98590490
7	FOS	chr10:98590362-98590609	MCF10A-Er-Src	breast:	n/a	n/a
8	YY1	chr10:98590362-98590631	HCT-116	colon:	n/a	n/a
9	BCLAF1	chr10:98590196-98590741	GM12878	blood:	n/a	chr10:98590416-98590425
10	RAD21	chr10:98590270-98590665	HepG2	liver:	n/a	n/a
11	CTCF	chr10:98590402-98590603	GM12892	blood:	n/a	chr10:98590477-98590490
12	YY1	chr10:98590364-98590796	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr10:98590400-98590601	GM19239	blood:	n/a	chr10:98590477-98590490
14	RFX5	chr10:98590215-98590631	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr10:98590369-98590633	MCF-7	breast:	n/a	chr10:98590477-98590490
16	RCOR1	chr10:98590266-98590946	K562	blood:	n/a	n/a
17	CTCF	chr10:98590369-98590625	GM10248	blood:	n/a	chr10:98590477-98590490
18	CTCF	chr10:98590440-98590590	HepG2	liver:	n/a	chr10:98590477-98590490
19	CTCF	chr10:98590420-98590570	GM12875	blood:	n/a	chr10:98590477-98590490
20	CTCF	chr10:98590266-98590631	A549	lung:	n/a	chr10:98590477-98590490
21	CTCF	chr10:98590440-98590590	WI-38	lung:	n/a	chr10:98590477-98590490
22	YY1	chr10:98590344-98590716	GM12892	blood:	n/a	n/a
23	CTCF	chr10:98590382-98590614	MCF-7	breast:	n/a	chr10:98590477-98590490
24	RAD21	chr10:98590242-98590647	GM12878	blood:	n/a	n/a
25	SMC3	chr10:98589938-98590749	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr10:98590225-98590685	T-47D	breast:	n/a	chr10:98590477-98590490
27	CTCF	chr10:98590384-98590619	Kidney_OC	kidney:	n/a	chr10:98590477-98590490
28	CTCF	chr10:98590440-98590590	GM12878	blood:	n/a	chr10:98590477-98590490
29	EP300	chr10:98589861-98590799	K562	blood:	n/a	chr10:98590495-98590504
30	RCOR1	chr10:98590352-98590651	GM12878	blood:	n/a	n/a
31	MYC	chr10:98590353-98590636	NB4	blood:	n/a	n/a
32	TBL1XR1	chr10:98590328-98590665	K562	blood:	n/a	n/a
33	CTCF	chr10:98590420-98590570	AG09309	skin:	n/a	chr10:98590477-98590490
34	CTCF	chr10:98590420-98590570	RPTEC	kidney:	n/a	chr10:98590477-98590490
35	RAD21	chr10:98590212-98590691	MCF-7	breast:	n/a	n/a
36	MAX	chr10:98590411-98590704	H1-hESC	embryonic stem cell:	n/a	n/a
37	STAT3	chr10:98590538-98590704	MCF10A-Er-Src	breast:	n/a	chr10:98590615-98590638
38	SMC3	chr10:98590313-98590636	K562	blood:	n/a	n/a
39	CTCF	chr10:98590302-98590665	A549	lung:	n/a	chr10:98590477-98590490
40	CTCF	chr10:98590322-98590628	SK-N-SH_RA	brain:	n/a	chr10:98590477-98590490
41	CTCF	chr10:98590279-98590644	K562	blood:	n/a	chr10:98590477-98590490
42	YY1	chr10:98590344-98590695	A549	lung:	n/a	n/a
43	POLR2A	chr10:98590498-98591063	K562	blood:	n/a	n/a
44	MYC	chr10:98590378-98590654	MCF10A-Er-Src	breast:	n/a	n/a
45	CTCF	chr10:98590380-98590603	GM13976	blood:	n/a	chr10:98590477-98590490
46	STAT3	chr10:98590456-98590620	MCF10A-Er-Src	breast:	n/a	n/a
47	GTF2F1	chr10:98590422-98590594	Hela-S3	cervix:	n/a	n/a
48	RAD21	chr10:98590320-98590694	H1-hESC	embryonic stem cell:	n/a	n/a
49	SIN3A	chr10:98590380-98590627	H1-hESC	embryonic stem cell:	n/a	chr10:98590592-98590606
50	YY1	chr10:98590295-98590751	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:98524912..98526111-chr10:98589792..98591303,11	MCF-7	breast:
2	chr10:98402475..98403373-chr10:98589917..98590679,3	MCF-7	breast:
3	chr10:98590420..98592007-chr10:98615843..98619097,3	K562	blood:
4	chr10:98549134..98550000-chr10:98589983..98590943,3	K562	blood:
5	chr10:98398475..98400373-chr10:98590281..98591916,2	MCF-7	breast:
6	chr10:98392223..98394189-chr10:98590324..98593027,3	MCF-7	breast:
7	chr10:98525204..98525891-chr10:98589963..98590854,2	K562	blood:
8	chr10:98584665..98586917-chr10:98589906..98591474,2	K562	blood:
9	chr10:98523538..98526378-chr10:98589191..98591883,2	MCF-7	breast:
10	chr10:98400341..98400974-chr10:98590389..98590915,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIK3AP1-6	chr10:98590424-98592003	NONHSAT015837

Variant related genes	Relation type
LCOR	TF binding region
MIR607	TF binding region
ENSG00000155629	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv895910	chr10:98386483-98640994	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1053801	chr10:98506832-98610101	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv825532	chr10:98567434-98618034	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
5	esv3427855	chr10:98590262-98594060	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98587200-98591400	Weak transcription	Left Ventricle	heart
2	chr10:98588200-98591000	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr10:98589000-98591000	Enhancers	HepG2	liver
4	chr10:98589200-98591000	Enhancers	Duodenum Mucosa	Duodenum
5	chr10:98589200-98591000	Weak transcription	HSMMtube	muscle
6	chr10:98589200-98591200	Enhancers	Primary B cells from peripheral blood	blood
7	chr10:98589800-98591000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:98589800-98591000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr10:98590000-98590800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr10:98590000-98591000	Enhancers	Primary B cells from cord blood	blood
11	chr10:98590000-98591000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr10:98590000-98591000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr10:98590000-98591000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:98590000-98591000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:98590000-98591000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:98590000-98591000	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr10:98590000-98591000	Enhancers	A549	lung
18	chr10:98590000-98591000	Enhancers	Osteobl	bone
19	chr10:98590000-98591200	Enhancers	Primary T cells from cord blood	blood
20	chr10:98590000-98591200	Enhancers	Primary hematopoietic stem cells	blood
21	chr10:98590000-98591200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr10:98590000-98591200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:98590000-98591200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr10:98590000-98591200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr10:98590000-98591400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:98590000-98591400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:98590000-98591400	Enhancers	Small Intestine	intestine
28	chr10:98590000-98591600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:98590000-98591600	Enhancers	Stomach Mucosa	stomach
30	chr10:98590200-98590600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:98590200-98590600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:98590200-98590600	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr10:98590200-98590800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:98590200-98590800	Enhancers	NHDF-Ad	bronchial
35	chr10:98590200-98591000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr10:98590200-98591000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr10:98590200-98591000	Enhancers	HMEC	breast
38	chr10:98590200-98591000	Enhancers	NHEK	skin
39	chr10:98590200-98591200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:98590200-98591200	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr10:98590200-98591200	Enhancers	Colon Smooth Muscle	Colon
42	chr10:98590200-98591200	Enhancers	Fetal Intestine Small	intestine
43	chr10:98590200-98594600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr10:98590400-98590600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
45	chr10:98590400-98590600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr10:98590400-98590600	Flanking Active TSS	Liver	Liver
47	chr10:98590400-98590800	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr10:98590400-98590800	Enhancers	GM12878-XiMat	blood
49	chr10:98590400-98590800	Active TSS	K562	blood
50	chr10:98590400-98591000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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