Variant report

Variant	rs553162479
Chromosome Location	chr9:94902676-94902677
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	E2F6	chr9:94902628-94903008	A549	lung:	n/a	chr9:94902748-94902759
2	RAD21	chr9:94902618-94902942	K562	blood:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
3	RAD21	chr9:94902587-94902943	K562	blood:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
4	MAX	chr9:94902586-94903110	HepG2	liver:	n/a	n/a
5	CTCF	chr9:94902640-94902790	GM12870	blood:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
6	STAT1	chr9:94902620-94902855	GM12878	blood:	n/a	n/a
7	CHD2	chr9:94902672-94902914	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr9:94902640-94902790	HCT-116	colon:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
9	MAX	chr9:94902560-94903108	HCT-116	colon:	n/a	n/a
10	MAX	chr9:94902565-94903100	A549	lung:	n/a	n/a
11	MXI1	chr9:94902467-94903909	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr9:94902660-94902810	Hela-S3	cervix:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
13	NFIC	chr9:94902622-94902868	HepG2	liver:	n/a	n/a
14	CTCF	chr9:94902640-94902790	NHEK	skin:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
15	CTCF	chr9:94902604-94902851	H1-hESC	embryonic stem cell:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
16	CTCF	chr9:94902444-94903129	HCT-116	colon:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
17	RAD21	chr9:94902528-94902920	H1-hESC	embryonic stem cell:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
18	WRNIP1	chr9:94902604-94902804	GM12878	blood:	n/a	n/a
19	CTCF	chr9:94902640-94902790	SK-N-SH_RA	brain:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
20	CTCF	chr9:94902660-94902810	AG10803	skin:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
21	RAD21	chr9:94902503-94903189	HCT-116	colon:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
22	RAD21	chr9:94902612-94902903	SK-N-SH_RA	brain:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
23	CTCF	chr9:94902660-94902810	NHLF	lung:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
24	CTCFL	chr9:94902667-94902842	K562	blood:	n/a	chr9:94902746-94902755
25	RAD21	chr9:94902517-94902971	ECC-1	luminal epithelium:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
26	TEAD4	chr9:94902576-94902933	H1-hESC	embryonic stem cell:	n/a	n/a
27	MYC	chr9:94902630-94902930	K562	blood:	n/a	n/a
28	JUN	chr9:94902595-94902983	K562	blood:	n/a	n/a
29	CTCF	chr9:94902660-94902810	NHDF-neo	bronchial:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
30	MAX	chr9:94902618-94902961	NB4	blood:	n/a	n/a
31	CTCF	chr9:94902660-94902810	BJ	skin:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
32	CTCF	chr9:94902475-94902934	A549	lung:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
33	MYBL2	chr9:94902488-94902986	HepG2	liver:	n/a	n/a
34	TBL1XR1	chr9:94902624-94902847	K562	blood:	n/a	n/a
35	PBX3	chr9:94902648-94902867	GM12878	blood:	n/a	n/a
36	CTCF	chr9:94902516-94902916	K562	blood:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
37	MAX	chr9:94902630-94902939	K562	blood:	n/a	n/a
38	SIN3AK20	chr9:94902590-94902889	SK-N-SH	brain:	n/a	n/a
39	CTCF	chr9:94902660-94902810	AoAF	blood vessel:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
40	MAX	chr9:94902556-94903030	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr9:94902611-94903031	A549	lung:	n/a	chr9:94902741-94902755 chr9:94902740-94902759 chr9:94902741-94902750
42	CTCF	chr9:94902640-94902790	HEK293	kidney:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
43	MAX	chr9:94902641-94902917	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr9:94902533-94902970	H1-hESC	embryonic stem cell:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
45	CTCF	chr9:94902660-94902810	AG09309	skin:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
46	MAX	chr9:94902610-94902970	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr9:94902660-94902810	HMF	breast:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
48	CTCF	chr9:94902530-94902911	GM12878	blood:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752
49	BCLAF1	chr9:94902534-94902978	GM12878	blood:	n/a	n/a
50	CTCF	chr9:94902577-94902877	Lung_OC	lung:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752

No.	Distal block	Cell Line	Cell type
1	chr9:94900325..94903739-chr9:94909399..94912070,4	MCF-7	breast:
2	chr9:94902262..94903203-chr9:95396707..95397642,2	K562	blood:
3	chr1:117477349..117478025-chr9:94902653..94903339,2	MCF-7	breast:
4	chr9:94902342..94903195-chr9:95004476..95005483,4	MCF-7	breast:
5	chr9:94901685..94904988-chr9:95003695..95006795,3	MCF-7	breast:
6	chr9:94898906..94903668-chr9:95086648..95090271,5	MCF-7	breast:
7	chr9:94902503..94903236-chr9:95396725..95397397,2	MCF-7	breast:
8	chr9:94902223..94905302-chr9:94908199..94910430,4	MCF-7	breast:
9	chr9:94902180..94903465-chr9:95004247..95005390,7	MCF-7	breast:

Variant related genes	Relation type
LINC00475	TF binding region
ENSG00000225511	Chromatin interaction
ENSG00000196305	Chromatin interaction
ENSG00000188312	Chromatin interaction
ENSG00000198000	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv972778	chr9:94902068-94908273	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94896600-94902800	Weak transcription	Gastric	stomach
2	chr9:94896800-94902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:94896800-94902800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:94896800-94902800	Weak transcription	Esophagus	oesophagus
5	chr9:94896800-94902800	Weak transcription	Right Atrium	heart
6	chr9:94896800-94902800	Weak transcription	A549	lung
7	chr9:94897200-94902800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:94897200-94902800	Weak transcription	HUVEC	blood vessel
9	chr9:94897400-94902800	Weak transcription	NHDF-Ad	bronchial
10	chr9:94897600-94902800	Weak transcription	HMEC	breast
11	chr9:94900000-94903000	Flanking Active TSS	HepG2	liver
12	chr9:94900200-94903200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:94900400-94902800	Weak transcription	Hela-S3	cervix
14	chr9:94900400-94902800	Weak transcription	K562	blood
15	chr9:94900800-94903000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:94900800-94903000	Enhancers	HSMMtube	muscle
17	chr9:94901000-94902800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:94901600-94902800	Weak transcription	NH-A	brain
19	chr9:94902000-94903000	Enhancers	NHLF	lung
20	chr9:94902200-94902800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:94902200-94902800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:94902200-94902800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:94902200-94902800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr9:94902200-94902800	Enhancers	HSMM	muscle
25	chr9:94902200-94903000	Enhancers	Placenta	Placenta
26	chr9:94902200-94903200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:94902200-94904200	Enhancers	Liver	Liver
28	chr9:94902400-94902800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr9:94902400-94902800	Enhancers	Primary B cells from peripheral blood	blood
30	chr9:94902400-94902800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:94902400-94902800	Enhancers	Muscle Satellite Cultured Cells	--
32	chr9:94902400-94902800	Enhancers	Colonic Mucosa	Colon
33	chr9:94902400-94902800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr9:94902400-94902800	Enhancers	Ovary	ovary
35	chr9:94902400-94902800	Enhancers	Pancreas	Pancrea
36	chr9:94902400-94902800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
37	chr9:94902400-94902800	Enhancers	Osteobl	bone
38	chr9:94902400-94903000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr9:94902400-94903000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:94902400-94903000	Enhancers	Placenta Amnion	Placenta Amnion
41	chr9:94902400-94903000	Enhancers	Spleen	Spleen
42	chr9:94902400-94903200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:94902400-94903200	Bivalent Enhancer	Fetal Stomach	stomach
44	chr9:94902600-94902800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr9:94902600-94902800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr9:94902600-94902800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
47	chr9:94902600-94902800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:94902600-94902800	Bivalent Enhancer	Adipose Nuclei	Adipose
49	chr9:94902600-94902800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
50	chr9:94902600-94902800	Bivalent Enhancer	Duodenum Mucosa	Duodenum

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