Variant report

Variant	rs552568914
Chromosome Location	chr9:137000687-137000688
allele	A/C
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	TAF1	chr9:137000098-137001417	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr9:137000391-137001959	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr9:137000660-137000810	HBMEC	blood vessel:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
4	POLR2A	chr9:137000122-137001241	U87	brain:	n/a	n/a
5	POLR2A	chr9:137000267-137000782	PANC-1	pancreas:	n/a	n/a
6	TAF1	chr9:137000398-137001388	GM12878	blood:	n/a	n/a
7	TCF7L2	chr9:137000482-137001160	HCT-116	colon:	n/a	n/a
8	NFIC	chr9:137000363-137000689	HepG2	liver:	n/a	n/a
9	TAF1	chr9:137000663-137001389	K562	blood:	n/a	n/a
10	POLR2A	chr9:136999908-137002325	Hela-S3	cervix:	n/a	n/a
11	UBTF	chr9:136999905-137001239	K562	blood:	n/a	n/a
12	CTCF	chr9:137000660-137000810	HCFaa	heart:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
13	RELA	chr9:137000553-137001233	GM19099	blood:	n/a	n/a
14	TBP	chr9:137000373-137001257	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr9:137000640-137000790	AG09319	gingival:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
16	CTCF	chr9:137000660-137000810	RPTEC	kidney:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
17	POLR2A	chr9:136999899-137003166	HepG2	liver:	n/a	n/a
18	POLR2A	chr9:137000281-137001310	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr9:136999821-137001428	K562	blood:	n/a	n/a
20	NRF1	chr9:137000175-137001385	GM12878	blood:	n/a	chr9:137000877-137000888 chr9:137000507-137000516 chr9:137001185-137001199 chr9:137001188-137001197 chr9:137001188-137001199 chr9:137001158-137001167 chr9:137001188-137001202
21	CTCF	chr9:137000680-137000830	NHDF-neo	bronchial:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
22	CHD2	chr9:137000385-137001992	Hela-S3	cervix:	n/a	chr9:137001849-137001859 chr9:137001156-137001166
23	CTCF	chr9:137000640-137000790	SK-N-SH_RA	brain:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
24	CTCF	chr9:137000625-137000827	MCF-7	breast:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764 chr9:137000627-137000640
25	CTCF	chr9:137000620-137000770	HA-sp	spinal cord:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764 chr9:137000627-137000640
26	PML	chr9:137000236-137001333	GM12878	blood:	n/a	n/a
27	IRF1	chr9:136999999-137001295	K562	blood:	n/a	chr9:137001154-137001168
28	POLR2A	chr9:137000331-137002161	GM12878	blood:	n/a	n/a
29	CTCF	chr9:137000620-137000770	HMEC	breast:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764 chr9:137000627-137000640
30	CTCF	chr9:137000634-137000818	MCF-7	breast:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
31	HEY1	chr9:137000108-137001522	HepG2	liver:	n/a	chr9:137000546-137000561 chr9:137001328-137001343 chr9:137001359-137001374 chr9:137001202-137001217 chr9:137000612-137000627
32	ELF1	chr9:137000234-137001347	GM12878	blood:	n/a	n/a
33	TCF12	chr9:137000549-137001236	ECC-1	luminal epithelium:	n/a	n/a
34	CTCF	chr9:137000580-137000730	BE2_C	brain:	n/a	chr9:137000627-137000640
35	CTCF	chr9:137000600-137000750	HCT-116	colon:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000627-137000640
36	POLR2A	chr9:136999710-137001492	K562	blood:	n/a	n/a
37	TBP	chr9:136999770-137001266	K562	blood:	n/a	n/a
38	STAT1	chr9:137000302-137001184	GM12878	blood:	n/a	n/a
39	YY1	chr9:137000216-137001551	HepG2	liver:	n/a	chr9:137000546-137000557 chr9:137001204-137001218 chr9:137001220-137001234 chr9:137001203-137001214 chr9:137001158-137001167 chr9:137001203-137001212 chr9:137001206-137001215
40	MAZ	chr9:137000563-137001293	HepG2	liver:	n/a	n/a
41	TAF1	chr9:137000165-137001404	Hela-S3	cervix:	n/a	n/a
42	RUNX3	chr9:137000520-137001149	GM12878	blood:	n/a	n/a
43	POLR2A	chr9:137000193-137002010	GM19099	blood:	n/a	n/a
44	CTCF	chr9:137000660-137000810	Caco-2	colon:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
45	BCL3	chr9:137000637-137001219	A549	lung:	n/a	chr9:137001205-137001214 chr9:137001206-137001219
46	CTCF	chr9:137000600-137000750	GM12874	blood:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000627-137000640
47	CTCF	chr9:137000640-137000790	AG04449	skin:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764
48	TAF1	chr9:137000553-137000836	GM12892	blood:	n/a	n/a
49	TAF1	chr9:137000255-137000946	HepG2	liver:	n/a	n/a
50	CTCF	chr9:137000613-137000897	GM19240	blood:	n/a	chr9:137000726-137000739 chr9:137000723-137000741 chr9:137000751-137000764 chr9:137000627-137000640

No.	Distal block	Cell Line	Cell type
1	chr16:401149..403748-chr9:137000262..137001904,2	MCF-7	breast:
2	chr2:220091886..220094259-chr9:137000513..137003179,2	MCF-7	breast:
3	chr9:136930118..136934023-chr9:136998387..137002829,10	K562	blood:
4	chr9:136931194..136934944-chr9:136998387..137002829,6	K562	blood:
5	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
6	chr9:136930108..136935337-chr9:136999374..137002737,14	MCF-7	breast:
7	chr9:136997943..137000936-chr9:137029556..137031957,3	K562	blood:
8	chr9:136919895..136922369-chr9:137000361..137002123,2	MCF-7	breast:
9	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
10	chr9:136282958..136284963-chr9:136998714..137001684,2	K562	blood:
11	chr9:136889824..136891845-chr9:137000522..137002324,2	K562	blood:
12	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
13	chr9:136888792..136891646-chr9:137000403..137003499,3	MCF-7	breast:
14	chr9:136999192..137001560-chr9:137216028..137218729,4	MCF-7	breast:
15	chr9:137000678..137001573-chr9:137029002..137029689,2	Hela-S3	cervix:
16	chr9:137000635..137002837-chr9:137296498..137299052,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BRD3-1	chr9:137000308-137001037	XLOC_007882
2	lnc-BRD3-1	chr9:137000308-137000771	ENSG00000273249.1
3	lnc-BRD3-1	chr9:137000308-137000894	ENSG00000273249.1

Variant related genes	Relation type
WDR5	TF binding region
ENSG00000235106	Chromatin interaction
ENSG00000103126	Chromatin interaction
ENSG00000198925	Chromatin interaction
ENSG00000169925	Chromatin interaction
ENSG00000186350	Chromatin interaction
ENSG00000221676	Chromatin interaction
ENSG00000148300	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
9	esv3392543	chr9:137000156-137002904	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	esv3444727	chr9:137000331-137002454	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136999400-137001600	Active TSS	Colonic Mucosa	Colon
2	chr9:136999600-137002000	Active TSS	Lung	lung
3	chr9:136999600-137002400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr9:136999800-137000800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:136999800-137001800	Active TSS	Gastric	stomach
6	chr9:136999800-137002000	Active TSS	Left Ventricle	heart
7	chr9:136999800-137002400	Active TSS	Fetal Kidney	kidney
8	chr9:136999800-137002600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr9:136999800-137002600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:137000000-137000800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr9:137000000-137000800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr9:137000000-137001000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:137000000-137001000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr9:137000000-137001600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr9:137000000-137002000	Active TSS	Esophagus	oesophagus
16	chr9:137000000-137002000	Active TSS	Fetal Intestine Small	intestine
17	chr9:137000000-137002000	Active TSS	Psoas Muscle	Psoas
18	chr9:137000000-137002000	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr9:137000000-137002200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:137000000-137002200	Active TSS	Ovary	ovary
21	chr9:137000000-137002200	Active TSS	NHDF-Ad	bronchial
22	chr9:137000000-137002400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr9:137000200-137000800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:137000200-137001000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
25	chr9:137000200-137001000	Active TSS	Fetal Heart	heart
26	chr9:137000200-137001400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:137000200-137001600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:137000200-137001600	Active TSS	Primary T cells from cord blood	blood
29	chr9:137000200-137001600	Active TSS	Right Ventricle	heart
30	chr9:137000200-137001800	Active TSS	Brain Angular Gyrus	brain
31	chr9:137000200-137001800	Active TSS	Brain Substantia Nigra	brain
32	chr9:137000200-137001800	Active TSS	Fetal Brain Male	brain
33	chr9:137000200-137001800	Active TSS	Fetal Brain Female	brain
34	chr9:137000200-137002000	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr9:137000200-137002000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:137000200-137002000	Active TSS	Fetal Intestine Large	intestine
37	chr9:137000200-137002000	Active TSS	Fetal Lung	lung
38	chr9:137000200-137002000	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr9:137000200-137002000	Active TSS	Small Intestine	intestine
40	chr9:137000200-137002000	Active TSS	NHEK	skin
41	chr9:137000200-137002200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:137000200-137002200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:137000200-137002200	Active TSS	Colon Smooth Muscle	Colon
44	chr9:137000200-137002200	Active TSS	Pancreas	Pancrea
45	chr9:137000200-137002400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:137000200-137002400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr9:137000200-137002400	Active TSS	Aorta	Aorta
48	chr9:137000200-137002600	Active TSS	H9 Cell Line	embryonic stem cell
49	chr9:137000200-137002600	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr9:137000200-137002800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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