Variant report

Variant	rs559078951
Chromosome Location	chr9:103235289-103235290
allele	A/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	POLR2A	chr9:103235155-103235532	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr9:103235160-103235310	HMF	breast:	n/a	n/a
3	CTCF	chr9:103235200-103235350	WERI-Rb-1	eye:	n/a	n/a
4	CTCF	chr9:103235140-103235290	HRE	kidney:	n/a	n/a
5	CTCF	chr9:103235220-103235370	GM12864	blood:	n/a	n/a
6	ZBTB7A	chr9:103234996-103236749	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr9:103235279-103235360	GM19238	blood:	n/a	n/a
8	CTCF	chr9:103235200-103235350	AG04449	skin:	n/a	n/a
9	MAX	chr9:103234910-103235453	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr9:103235274-103235389	GM10248	blood:	n/a	n/a
11	CTCF	chr9:103235160-103235310	HFF-Myc	foreskin:	n/a	n/a
12	EGR1	chr9:103235108-103235440	K562	blood:	n/a	chr9:103235421-103235431 chr9:103235256-103235266
13	CTCF	chr9:103235240-103235390	NHDF-neo	bronchial:	n/a	n/a
14	MAX	chr9:103234906-103235421	A549	lung:	n/a	n/a
15	USF1	chr9:103235267-103235513	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr9:103235200-103235350	AG09319	gingival:	n/a	n/a
17	POLR2A	chr9:103235026-103237160	H1-hESC	embryonic stem cell:	n/a	n/a
18	USF2	chr9:103234774-103235483	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr9:103235200-103235350	SK-N-SH_RA	brain:	n/a	n/a
20	EGR1	chr9:103235210-103235372	GM12878	blood:	n/a	chr9:103235256-103235266
21	CTCF	chr9:103235200-103235350	GM12866	blood:	n/a	n/a
22	MAX	chr9:103234993-103236528	HepG2	liver:	n/a	chr9:103235778-103235788 chr9:103236482-103236497
23	CTCF	chr9:103235180-103235330	AG04450	lung:	n/a	n/a
24	CTCF	chr9:103235160-103235310	HPAF	blood vessel:	n/a	n/a
25	RAD21	chr9:103235146-103235361	HepG2	liver:	n/a	n/a
26	CTCF	chr9:103235285-103235345	GM19239	blood:	n/a	n/a
27	CTCF	chr9:103235237-103235353	SK-N-SH_RA	brain:	n/a	n/a
28	E2F6	chr9:103234881-103235475	H1-hESC	embryonic stem cell:	n/a	chr9:103235201-103235212
29	CTCF	chr9:103235228-103235408	MCF-7	breast:	n/a	chr9:103235384-103235397
30	TAF1	chr9:103235236-103235706	H1-neurons	neurons:	n/a	n/a
31	MAX	chr9:103234973-103235401	NB4	blood:	n/a	n/a
32	NRF1	chr9:103234909-103236049	SK-N-SH	brain:	n/a	chr9:103235263-103235272 chr9:103235421-103235430
33	HMGN3	chr9:103235240-103236365	K562	blood:	n/a	n/a
34	CTCF	chr9:103235238-103235395	MCF-7	breast:	n/a	n/a
35	SIN3AK20	chr9:103235101-103235471	SK-N-SH	brain:	n/a	n/a
36	MYC	chr9:103234920-103235370	NB4	blood:	n/a	n/a
37	CTCF	chr9:103235160-103235310	WERI-Rb-1	eye:	n/a	n/a
38	REST	chr9:103234842-103237848	H1-neurons	neurons:	n/a	chr9:103235650-103235663 chr9:103235342-103235352 chr9:103235674-103235687 chr9:103235709-103235722 chr9:103235355-103235368 chr9:103235779-103235792 chr9:103236454-103236467
39	CTCF	chr9:103235140-103235290	GM06990	blood:	n/a	n/a
40	CTCF	chr9:103235240-103235390	HFF	foreskin:	n/a	n/a
41	CTCF	chr9:103235265-103235384	Fibrobl	skin:	n/a	n/a
42	CTCF	chr9:103235200-103235350	HepG2	liver:	n/a	n/a
43	CTCF	chr9:103235200-103235350	GM12870	blood:	n/a	n/a
44	ZNF143	chr9:103235061-103235458	H1-hESC	embryonic stem cell:	n/a	chr9:103235343-103235353 chr9:103235258-103235268
45	CTCF	chr9:103235240-103235390	AG09319	gingival:	n/a	n/a
46	ZBTB7A	chr9:103235179-103235397	HepG2	liver:	n/a	n/a
47	MAZ	chr9:103235133-103236129	K562	blood:	n/a	chr9:103235778-103235788
48	CREB1	chr9:103235114-103235584	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr9:103234868-103237304	H1-neurons	neurons:	n/a	n/a
50	CTCF	chr9:103235200-103235350	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:103187999..103190908-chr9:103233595..103236918,6	MCF-7	breast:
2	chr9:103188255..103190992-chr9:103234182..103236159,2	MCF-7	breast:
3	chr9:103113352..103115792-chr9:103234740..103236804,2	K562	blood:

Variant related genes	Relation type
TMEFF1	TF binding region
ENSG00000136891	Chromatin interaction
ENSG00000066697	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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3348068	chr9:103234431-103236904	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3376333	chr9:103234756-103237304	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103232200-103235400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:103234600-103235400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:103234600-103236600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:103234600-103237400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr9:103234600-103237400	Active TSS	Fetal Kidney	kidney
6	chr9:103234800-103235400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:103234800-103235800	Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr9:103234800-103235800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:103234800-103235800	Enhancers	Placenta	Placenta
10	chr9:103234800-103235800	Active TSS	Fetal Stomach	stomach
11	chr9:103234800-103236400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr9:103234800-103236400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:103234800-103236400	Bivalent/Poised TSS	Thymus	Thymus
14	chr9:103234800-103236600	Active TSS	Primary T cells from cord blood	blood
15	chr9:103234800-103236600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr9:103234800-103236600	Active TSS	NH-A	brain
17	chr9:103234800-103237000	Active TSS	Brain Cingulate Gyrus	brain
18	chr9:103234800-103237400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:103234800-103237400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:103234800-103237400	Active TSS	Brain Germinal Matrix	brain
21	chr9:103235000-103235400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:103235000-103235400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr9:103235000-103235600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:103235000-103235600	Enhancers	Spleen	Spleen
25	chr9:103235000-103235800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:103235000-103235800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:103235000-103235800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:103235000-103235800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:103235000-103235800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:103235000-103235800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
31	chr9:103235000-103235800	Bivalent/Poised TSS	Esophagus	oesophagus
32	chr9:103235000-103235800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr9:103235000-103235800	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr9:103235000-103235800	Active TSS	Right Ventricle	heart
35	chr9:103235000-103236000	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
36	chr9:103235000-103236000	Active TSS	Fetal Muscle Trunk	muscle
37	chr9:103235000-103236000	Active TSS	Left Ventricle	heart
38	chr9:103235000-103236000	Active TSS	Pancreas	Pancrea
39	chr9:103235000-103236000	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr9:103235000-103236400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:103235000-103236400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chr9:103235000-103236400	Active TSS	Ovary	ovary
43	chr9:103235000-103236400	Active TSS	Stomach Smooth Muscle	stomach
44	chr9:103235000-103236600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:103235000-103236600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:103235000-103236600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr9:103235000-103236600	Active TSS	Aorta	Aorta
48	chr9:103235000-103236600	Active TSS	Psoas Muscle	Psoas
49	chr9:103235000-103236600	Active TSS	Rectal Smooth Muscle	rectum
50	chr9:103235000-103236600	Active TSS	HMEC	breast

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