Variant report

Variant	nsv580966
Chromosome Location	chr2:10588031-10588138
allele	n/a
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	ARID3A	chr2:10588104-10588185	K562	blood:	n/a	n/a
2	ATF3	chr2:10587944-10588307	HepG2	liver:	n/a	chr2:10587963-10587972
3	BCL3	chr2:10587992-10588612	GM12878	blood:	n/a	chr2:10588309-10588322 chr2:10588222-10588231 chr2:10588262-10588275
4	BCLAF1	chr2:10587426-10588480	GM12878	blood:	n/a	chr2:10588309-10588322 chr2:10588222-10588231 chr2:10588262-10588275
5	BHLHE40	chr2:10587939-10589085	HepG2	liver:	n/a	n/a
6	BHLHE40	chr2:10587766-10589275	K562	blood:	n/a	n/a
7	BHLHE40	chr2:10587981-10588510	A549	lung:	n/a	n/a
8	BHLHE40	chr2:10587527-10589296	GM12878	blood:	n/a	n/a
9	BRCA1	chr2:10588054-10588211	H1-hESC	embryonic stem cell:	n/a	n/a
10	CCNT2	chr2:10587645-10589227	K562	blood:	n/a	chr2:10588665-10588674
11	CEBPB	chr2:10587868-10588043	K562	blood:	n/a	n/a
12	CEBPB	chr2:10587812-10589049	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr2:10587787-10588116	HepG2	liver:	n/a	n/a
14	CEBPB	chr2:10587911-10588179	H1-hESC	embryonic stem cell:	n/a	n/a
15	CHD1	chr2:10586355-10588647	IMR90	lung:	n/a	n/a
16	CHD1	chr2:10586760-10588522	GM12878	blood:	n/a	n/a
17	CHD2	chr2:10587546-10589316	GM12878	blood:	n/a	n/a
18	CHD2	chr2:10587479-10589205	K562	blood:	n/a	n/a
19	CHD2	chr2:10587612-10589347	Hela-S3	cervix:	n/a	n/a
20	CHD2	chr2:10587585-10589145	HepG2	liver:	n/a	n/a
21	CHD2	chr2:10587612-10588195	H1-hESC	embryonic stem cell:	n/a	n/a
22	CREB1	chr2:10587989-10589287	K562	blood:	n/a	n/a
23	CREB1	chr2:10587736-10589114	A549	lung:	n/a	n/a
24	CREB1	chr2:10587447-10589563	HepG2	liver:	n/a	n/a
25	CTCF	chr2:10587900-10588050	GM12874	blood:	n/a	n/a
26	CTCF	chr2:10587920-10588070	HFF	foreskin:	n/a	n/a
27	CTCF	chr2:10587900-10588050	GM12866	blood:	n/a	n/a
28	CTCF	chr2:10587900-10588050	GM12878	blood:	n/a	n/a
29	E2F1	chr2:10587725-10589527	Hela-S3	cervix:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
30	E2F4	chr2:10587924-10589264	K562	blood:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
31	E2F6	chr2:10587717-10589474	K562	blood:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
32	E2F6	chr2:10587425-10589683	H1-hESC	embryonic stem cell:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
33	E2F6	chr2:10587674-10588546	A549	lung:	n/a	chr2:10587961-10587970 chr2:10588257-10588267
34	E2F6	chr2:10587846-10589293	K562	blood:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
35	E2F6	chr2:10587648-10589423	H1-hESC	embryonic stem cell:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
36	E2F6	chr2:10587795-10589268	K562	blood:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
37	E2F6	chr2:10587444-10589563	A549	lung:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
38	E2F6	chr2:10587867-10589406	Hela-S3	cervix:	n/a	chr2:10588665-10588674 chr2:10587961-10587970 chr2:10588257-10588267 chr2:10588788-10588797
39	EBF1	chr2:10588054-10588503	GM12878	blood:	n/a	chr2:10588273-10588284
40	EBF1	chr2:10588046-10588653	GM12878	blood:	n/a	chr2:10588273-10588284
41	EGR1	chr2:10588088-10588755	GM12878	blood:	n/a	chr2:10588664-10588674
42	EGR1	chr2:10588110-10589327	GM12878	blood:	n/a	chr2:10589119-10589129 chr2:10589119-10589128 chr2:10589119-10589129 chr2:10589117-10589132 chr2:10589110-10589123 chr2:10589118-10589131 chr2:10588664-10588674 chr2:10589118-10589131 chr2:10589118-10589131 chr2:10588787-10588796 chr2:10589117-10589131 chr2:10589260-10589273 chr2:10588788-10588797
43	EGR1	chr2:10588067-10589379	K562	blood:	n/a	chr2:10589119-10589129 chr2:10589119-10589128 chr2:10589119-10589129 chr2:10589117-10589132 chr2:10589110-10589123 chr2:10589118-10589131 chr2:10588664-10588674 chr2:10589118-10589131 chr2:10589118-10589131 chr2:10588787-10588796 chr2:10589117-10589131 chr2:10589260-10589273 chr2:10588788-10588797
44	EGR1	chr2:10587976-10588449	H1-hESC	embryonic stem cell:	n/a	n/a
45	EGR1	chr2:10588015-10589646	HCT-116	colon:	n/a	chr2:10589119-10589129 chr2:10589119-10589128 chr2:10589119-10589129 chr2:10589117-10589132 chr2:10589110-10589123 chr2:10589118-10589131 chr2:10588664-10588674 chr2:10589118-10589131 chr2:10589118-10589131 chr2:10588787-10588796 chr2:10589117-10589131 chr2:10589260-10589273 chr2:10588788-10588797
46	EGR1	chr2:10588016-10589360	K562	blood:	n/a	chr2:10589119-10589129 chr2:10589119-10589128 chr2:10589119-10589129 chr2:10589117-10589132 chr2:10589110-10589123 chr2:10589118-10589131 chr2:10588664-10588674 chr2:10589118-10589131 chr2:10589118-10589131 chr2:10588787-10588796 chr2:10589117-10589131 chr2:10589260-10589273 chr2:10588788-10588797
47	ELF1	chr2:10588086-10588407	K562	blood:	n/a	n/a
48	ELF1	chr2:10587976-10589157	K562	blood:	n/a	chr2:10588664-10588676
49	ELF1	chr2:10587776-10589540	GM12878	blood:	n/a	chr2:10588664-10588676 chr2:10587922-10587934 chr2:10587865-10587877
50	ELF1	chr2:10587716-10588670	GM12878	blood:	n/a	chr2:10587922-10587934 chr2:10587865-10587877

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:10588068-10588118	HNPCEpiC	eye:	n/a
2	chr2:10588068-10588118	H1-hESC	embryonic stem cell:	embryo
3	chr2:10588068-10588118	GM12878	blood:	n/a
4	chr2:10588068-10588118	AG10803	skin:	n/a
5	chr2:10588068-10588118	NB4	blood:	n/a
6	chr2:10588068-10588118	HEEpiC	esophagus:	n/a
7	chr2:10588068-10588118	HCPEpiC	choroid plexus:	n/a
8	chr2:10588068-10588118	K562	blood:	n/a
9	chr2:10588068-10588118	PFSK-1	brain:	n/a
10	chr2:10588068-10588118	SK-N-SH	brain:	n/a
11	chr2:10588068-10588118	ProgFib	skin:	n/a
12	chr2:10588068-10588118	NH-A	brain:	n/a
13	chr2:10588068-10588118	AG04449	skin:	fetal
14	chr2:10588068-10588118	HCM	heart:	n/a
15	chr2:10588068-10588118	NHDF-neo	bronchial:	n/a
16	chr2:10588068-10588118	HRPEpiC	eye:	n/a
17	chr2:10588068-10588118	Hela-S3	cervix:	n/a
18	chr2:10588068-10588118	HPAEpiC	pulmonary alveolar:	n/a
19	chr2:10588068-10588118	GM12892	blood:	n/a
20	chr2:10588068-10588118	AG04450	lung:	fetal
21	chr2:10588068-10588118	BJ	skin:	n/a
22	chr2:10588068-10588118	PANC-1	pancreas:	n/a
23	chr2:10588068-10588118	SK-N-MC	brain:	n/a
24	chr2:10588068-10588118	CMK	blood:	n/a
25	chr2:10588068-10588118	PrEC	prostate:	n/a
26	chr2:10588068-10588118	U87	brain:	n/a
27	chr2:10588068-10588118	HUVEC	blood vessel:	n/a
28	chr2:10588068-10588118	GM19239	blood:	n/a
29	chr2:10588068-10588118	MCF-7	breast:	n/a
30	chr2:10588068-10588118	BE2_C	brain:	n/a
31	chr2:10588068-10588118	HEK293	kidney:	embryo
32	chr2:10588068-10588118	ECC-1	luminal epithelium:	n/a
33	chr2:10588068-10588118	AoSMC	blood vessel:	n/a
34	chr2:10588068-10588118	MCF10A-Er-Src	breast:	n/a
35	chr2:10588068-10588118	IMR90	lung:	fetal
36	chr2:10588068-10588118	SKMC	muscle:	n/a
37	chr2:10588068-10588118	GM12891	blood:	n/a
38	chr2:10588068-10588118	RPTEC	kidney:	n/a
39	chr2:10588068-10588118	HCF	heart:	n/a
40	chr2:10588068-10588118	NHBE	bronchial:	n/a
41	chr2:10588068-10588118	Jurkat	blood:	n/a
42	chr2:10588068-10588118	A549	lung:	n/a
43	chr2:10588068-10588118	HCT-116	colon:	n/a
44	chr2:10588068-10588118	GM06990	blood:	n/a
45	chr2:10588068-10588118	HRCEpiC	kidney:	n/a
46	chr2:10588068-10588118	HRE	kidney:	n/a
47	chr2:10588068-10588118	T-47D	breast:	n/a
48	chr2:10588068-10588118	ovcar-3	ovarian:	n/a
49	chr2:10588068-10588118	HMEC	breast:	n/a
50	chr2:10588068-10588118	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10259839..10264771-chr2:10582056..10590038,19	K562	blood:
2	chr2:10587837..10588679-chr9:136214618..136215524,2	Hela-S3	cervix:
3	chr2:10584788..10589777-chr2:10826863..10830293,6	K562	blood:
4	chr2:10259653..10265917-chr2:10585320..10590295,8	MCF-7	breast:
5	chr11:77184882..77185407-chr2:10587988..10588765,2	HCT-116	colon:
6	chr19:39897578..39898321-chr2:10587983..10588853,2	Hela-S3	cervix:
7	chr2:9982517..9985169-chr2:10586715..10588876,2	K562	blood:
8	chr2:10259710..10265084-chr2:10586364..10590442,7	MCF-7	breast:
9	chr17:56708807..56709356-chr2:10588054..10588762,2	Hela-S3	cervix:
10	chr2:10183697..10185477-chr2:10588092..10590281,2	K562	blood:
11	chr2:10191630..10196148-chr2:10586386..10589794,5	K562	blood:
12	chr2:10265245..10266788-chr2:10587089..10589177,2	K562	blood:
13	chr2:10441623..10444177-chr2:10587166..10588748,2	K562	blood:
14	chr1:204463219..204463852-chr2:10587588..10588349,2	Hela-S3	cervix:
15	chr18:32072933..32074749-chr2:10587681..10589883,2	MCF-7	breast:
16	chr2:10257984..10265070-chr2:10582045..10589780,17	K562	blood:
17	chr2:10441623..10444200-chr2:10586906..10588748,2	K562	blood:
18	chr2:10420712..10423243-chr2:10586890..10589076,2	K562	blood:
19	chr2:10586529..10589550-chr2:10592115..10595368,3	MCF-7	breast:
20	chr2:10588007..10588995-chr20:62587586..62588155,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000257135	TF binding region
ENSG00000217258	TF binding region
ODC1	TF binding region
SNORA80B	TF binding region
ENSG00000257135	CpG island
ENSG00000217258	CpG island
ODC1	CpG island
SNORA80B	CpG island
ENSG00000115756	chromatin interactions
ENSG00000149269	chromatin interactions
ENSG00000171848	chromatin interactions
ENSG00000148297	chromatin interactions
ENSG00000134769	chromatin interactions
ENSG00000115750	chromatin interactions
ENSG00000128016	chromatin interactions
ENSG00000198276	chromatin interactions
ENSG00000271787	chromatin interactions
ENSG00000133056	chromatin interactions
ENSG00000172059	chromatin interactions
ENSG00000217258	chromatin interactions
ENSG00000115761	chromatin interactions
ENSG00000272524	chromatin interactions
ENSG00000264030	chromatin interactions
ENSG00000212195	chromatin interactions
ENSG00000148303	chromatin interactions

Extended variants
information (count: 7 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs146435265	chr2:10588031-10588032	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	18 gene(s)	Overlapped CNVs	n/a
2	rs115030661	chr2:10588045-10588046	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	18 gene(s)	Overlapped CNVs	n/a
3	rs538382777	chr2:10588051-10588052	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	18 gene(s)	Overlapped CNVs	n/a
4	rs554745040	chr2:10588055-10588056	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	19 gene(s)	Overlapped CNVs	n/a
5	rs548782636	chr2:10588087-10588088	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	Overlapped CNVs	n/a
6	rs567195721	chr2:10588109-10588110	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	20 gene(s)	Overlapped CNVs	n/a
7	rs2302615	chr2:10588138-10588139	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	20 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Mental retardation	17847001	CNVD
Glioblastoma multiforme	21080181	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Cancer	20164920	CNVD
Neuroblastoma	21508638	CNVD
Breast cancer	17603634	CNVD
Cancer	16751803	CNVD
Neuroblastoma	16790693	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Ependymoma	16718352	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Bladder cancer	21909424	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Breast cancer	21804112	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Glioma	17123091	CNVD
Breast cancer	20409316	CNVD
Multiple myeloma	16616336	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923524	CNVD
Acute myeloid leukemia	21251322	CNVD

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10585600-10589000	Active TSS	GM12878-XiMat	blood
2	chr2:10586000-10589600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr2:10586200-10588200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr2:10586200-10588800	Active TSS	Fetal Muscle Trunk	muscle
5	chr2:10586200-10589000	Active TSS	HSMM	muscle
6	chr2:10586200-10589000	Active TSS	HSMMtube	muscle
7	chr2:10586200-10589800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:10586400-10588800	Active TSS	Colonic Mucosa	Colon
9	chr2:10586400-10589000	Active TSS	Hela-S3	cervix
10	chr2:10586600-10588200	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr2:10586600-10589000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr2:10586600-10589000	Active TSS	NHLF	lung
13	chr2:10586600-10589400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:10586600-10589400	Active TSS	Psoas Muscle	Psoas
15	chr2:10586600-10589800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:10586800-10588200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr2:10586800-10589400	Active TSS	Fetal Brain Female	brain
18	chr2:10586800-10589600	Active TSS	Lung	lung
19	chr2:10587000-10588800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:10587000-10589000	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr2:10587000-10589000	Active TSS	A549	lung
22	chr2:10587000-10589200	Active TSS	Brain Anterior Caudate	brain
23	chr2:10587000-10589400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:10587200-10588200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:10587200-10588200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr2:10587200-10588400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:10587200-10588800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:10587200-10589000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr2:10587200-10589200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:10587200-10589200	Active TSS	Fetal Intestine Small	intestine
31	chr2:10587200-10589600	Active TSS	Brain Angular Gyrus	brain
32	chr2:10587200-10589600	Active TSS	Small Intestine	intestine
33	chr2:10587200-10589800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr2:10587400-10588200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:10587400-10588200	Active TSS	Right Atrium	heart
36	chr2:10587400-10588800	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr2:10587400-10588800	Active TSS	Muscle Satellite Cultured Cells	--
38	chr2:10587400-10588800	Active TSS	Pancreas	Pancrea
39	chr2:10587400-10589400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:10587400-10589400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:10587400-10589400	Active TSS	Ovary	ovary
42	chr2:10587400-10589600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
43	chr2:10587400-10589600	Active TSS	H9 Cell Line	embryonic stem cell
44	chr2:10587400-10589600	Active TSS	Left Ventricle	heart
45	chr2:10587400-10589800	Active TSS	Right Ventricle	heart
46	chr2:10587600-10588200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
47	chr2:10587600-10588200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
48	chr2:10587600-10588400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:10587600-10588400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:10587600-10588800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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