Variant report

Variant	rs549908807
Chromosome Location	chr9:72287982-72287983
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	RCOR1	chr9:72287741-72288132	K562	blood:	n/a	n/a
2	CTCF	chr9:72287880-72288030	Hela-S3	cervix:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
3	CTCF	chr9:72287840-72287990	GM12870	blood:	n/a	chr9:72287953-72287962
4	CTCF	chr9:72287880-72288030	GM12869	blood:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
5	CTCF	chr9:72287860-72288010	A549	lung:	n/a	chr9:72287953-72287962
6	CTCF	chr9:72287880-72288030	WERI-Rb-1	eye:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
7	JUND	chr9:72287810-72288071	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr9:72287880-72288030	HVMF	connective:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
9	PBX3	chr9:72287631-72288208	SK-N-SH	brain:	n/a	n/a
10	MAZ	chr9:72287791-72288140	K562	blood:	n/a	n/a
11	CTCF	chr9:72287900-72288050	HepG2	liver:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
12	CTCF	chr9:72287802-72288093	SK-N-SH_RA	brain:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
13	PBX3	chr9:72287816-72288016	GM12878	blood:	n/a	n/a
14	CTCF	chr9:72287818-72288087	ProgFib	skin:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
15	CTCF	chr9:72287900-72288050	GM12864	blood:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
16	CTCF	chr9:72287940-72288090	RPTEC	kidney:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
17	CTCF	chr9:72287880-72288030	GM12868	blood:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
18	CTCF	chr9:72287799-72288098	Medullo	brain:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
19	RAD21	chr9:72287659-72288256	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr9:72287860-72288010	HAc	cerebellar:	n/a	chr9:72287953-72287962
21	CHD1	chr9:72287698-72288163	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr9:72287852-72288155	HepG2	liver:	n/a	n/a
23	CTCF	chr9:72287860-72288010	BJ	skin:	n/a	chr9:72287953-72287962
24	E2F6	chr9:72287676-72288096	A549	lung:	n/a	chr9:72287861-72287868 chr9:72287861-72287868 chr9:72287860-72287868 chr9:72287860-72287872 chr9:72287861-72287868
25	CTCF	chr9:72287860-72288010	GM12869	blood:	n/a	chr9:72287953-72287962
26	CTCF	chr9:72287840-72287990	HRE	kidney:	n/a	chr9:72287953-72287962
27	RAD21	chr9:72287773-72288217	HepG2	liver:	n/a	n/a
28	CTCF	chr9:72287759-72288155	T-47D	breast:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
29	CTCF	chr9:72287830-72288075	HUVEC	blood vessel:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
30	CTCF	chr9:72287832-72288082	GM10266	blood:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
31	RAD21	chr9:72287693-72288202	HepG2	liver:	n/a	n/a
32	MAX	chr9:72286708-72288222	SK-N-SH	brain:	n/a	chr9:72287424-72287434
33	CTCF	chr9:72287860-72288010	WI-38	lung:	n/a	chr9:72287953-72287962
34	TEAD4	chr9:72287648-72288215	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr9:72287742-72288239	MCF-7	breast:	n/a	chr9:72288204-72288214 chr9:72287953-72287962 chr9:72288010-72288019
36	CTCF	chr9:72287840-72287990	GM12864	blood:	n/a	chr9:72287953-72287962
37	CHD2	chr9:72287842-72288051	GM12878	blood:	n/a	n/a
38	CTCF	chr9:72287900-72288050	AG09319	gingival:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
39	CTCF	chr9:72287840-72287990	GM12865	blood:	n/a	chr9:72287953-72287962
40	TEAD4	chr9:72287693-72288223	ECC-1	luminal epithelium:	n/a	n/a
41	CTCF	chr9:72287677-72288263	HCT-116	colon:	n/a	chr9:72288204-72288214 chr9:72287953-72287962 chr9:72288010-72288019
42	REST	chr9:72287820-72288157	SK-N-SH	brain:	n/a	chr9:72288032-72288045
43	CTCF	chr9:72287860-72288010	HPF	lung:	n/a	chr9:72287953-72287962
44	CTCF	chr9:72287900-72288050	GM12872	blood:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
45	CTCF	chr9:72287555-72288102	GM12892	blood:	n/a	chr9:72287629-72287642 chr9:72287953-72287962 chr9:72288010-72288019
46	CTCF	chr9:72287840-72287990	HAc	cerebellar:	n/a	chr9:72287953-72287962
47	CTCF	chr9:72287809-72288092	Lung_OC	lung:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
48	GABPA	chr9:72287703-72288139	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr9:72287651-72288161	K562	blood:	n/a	chr9:72287953-72287962 chr9:72288010-72288019
50	CTCF	chr9:72287840-72287990	HRPEpiC	eye:	n/a	chr9:72287953-72287962

No.	Distal block	Cell Line	Cell type
1	chr9:72287056..72289421-chr9:72373634..72375235,2	MCF-7	breast:
2	chr9:72286195..72289118-chr9:72373474..72376010,3	MCF-7	breast:
3	chr3:144137145..144137665-chr9:72287895..72288430,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf135-2	chr9:72287665-72288629	ENSG00000261447.1

Variant related genes	Relation type
APBA1	TF binding region
ENSG00000188647	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471309	chr9:72273898-72410323	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv3389299	chr9:72286157-72289005	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3321912	chr9:72286882-72288180	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72285400-72288400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:72286000-72288200	Active TSS	Brain Substantia Nigra	brain
3	chr9:72286200-72288000	Active TSS	Colonic Mucosa	Colon
4	chr9:72286200-72288200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:72286200-72288200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr9:72286200-72288600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:72286400-72288000	Active TSS	Rectal Smooth Muscle	rectum
8	chr9:72286400-72288000	Active TSS	HSMM	muscle
9	chr9:72286400-72288200	Active TSS	Brain Cingulate Gyrus	brain
10	chr9:72286400-72288200	Active TSS	Brain Hippocampus Middle	brain
11	chr9:72286400-72288400	Active TSS	Aorta	Aorta
12	chr9:72286400-72288400	Active TSS	HSMMtube	muscle
13	chr9:72286400-72288600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr9:72286600-72288000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:72286600-72288000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:72286600-72288000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr9:72286600-72288000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr9:72286600-72288000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:72286600-72288000	Active TSS	Gastric	stomach
20	chr9:72286600-72288000	Active TSS	NHDF-Ad	bronchial
21	chr9:72286600-72288200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr9:72286600-72288200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:72286600-72288200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr9:72286600-72288200	Active TSS	Brain Angular Gyrus	brain
25	chr9:72286600-72288200	Active TSS	Fetal Lung	lung
26	chr9:72286600-72288200	Active TSS	Left Ventricle	heart
27	chr9:72286600-72288200	Bivalent/Poised TSS	Thymus	Thymus
28	chr9:72286600-72288400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr9:72286600-72288400	Active TSS	Fetal Kidney	kidney
30	chr9:72286600-72288400	Active TSS	Ovary	ovary
31	chr9:72286600-72288400	Active TSS	Psoas Muscle	Psoas
32	chr9:72286600-72288400	Active TSS	Right Atrium	heart
33	chr9:72286600-72288400	Active TSS	Right Ventricle	heart
34	chr9:72286600-72288600	Active TSS	Brain Anterior Caudate	brain
35	chr9:72286600-72288600	Active TSS	Fetal Brain Female	brain
36	chr9:72286800-72288000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:72286800-72288000	Active TSS	Small Intestine	intestine
38	chr9:72286800-72288000	Active TSS	NH-A	brain
39	chr9:72286800-72288200	Active TSS	H9 Cell Line	embryonic stem cell
40	chr9:72286800-72288200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:72286800-72288200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:72286800-72288200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:72286800-72288200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr9:72286800-72288200	Active TSS	Muscle Satellite Cultured Cells	--
45	chr9:72286800-72288200	Active TSS	Colon Smooth Muscle	Colon
46	chr9:72286800-72288200	Weak transcription	Fetal Heart	heart
47	chr9:72286800-72288200	Active TSS	NHLF	lung
48	chr9:72286800-72288400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:72287000-72288000	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr9:72287000-72288000	Active TSS	Lung	lung

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