Variant report

Variant	nsv900856
Chromosome Location	chr13:89824076-89922393
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	CEBPB	chr13:89870206-89870527	HepG2	liver:	n/a	chr13:89870358-89870367 chr13:89870358-89870369 chr13:89870356-89870367
2	CEBPB	chr13:89921156-89921403	HepG2	liver:	n/a	chr13:89921266-89921277
3	CEBPB	chr13:89856691-89857129	ECC-1	luminal epithelium:	n/a	chr13:89856807-89856824
4	CEBPB	chr13:89856664-89857107	ECC-1	luminal epithelium:	n/a	chr13:89856807-89856824
5	CEBPB	chr13:89893668-89893895	HepG2	liver:	n/a	n/a
6	CTCF	chr13:89907570-89907625	Medullo	brain:	n/a	n/a
7	CTCF	chr13:89873440-89873590	WERI-Rb-1	eye:	n/a	n/a
8	CTCF	chr13:89893140-89893290	GM12866	blood:	n/a	n/a
9	CTCF	chr13:89920420-89920570	HPF	lung:	n/a	n/a
10	E2F4	chr13:89858454-89858750	MCF10A-Er-Src	breast:	n/a	n/a
11	E2F4	chr13:89862284-89862740	MCF10A-Er-Src	breast:	n/a	n/a
12	E2F4	chr13:89886058-89886204	MCF10A-Er-Src	breast:	n/a	n/a
13	E2F4	chr13:89884837-89884998	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr13:89856319-89856519	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F4	chr13:89879725-89880049	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr13:89918486-89918648	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr13:89856527-89857222	ECC-1	luminal epithelium:	n/a	chr13:89856961-89856971
18	EP300	chr13:89922061-89922361	SK-N-SH_RA	brain:	n/a	n/a
19	EP300	chr13:89922037-89922308	SK-N-SH_RA	brain:	n/a	n/a
20	EP300	chr13:89856582-89857113	ECC-1	luminal epithelium:	n/a	chr13:89856961-89856971
21	EP300	chr13:89911319-89911555	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr13:89834322-89834358	Hela-S3	cervix:	n/a	n/a
23	FOS	chr13:89879625-89880031	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr13:89919971-89920332	MCF10A-Er-Src	breast:	n/a	chr13:89920146-89920154 chr13:89920147-89920154 chr13:89920145-89920155 chr13:89920145-89920155 chr13:89920146-89920154 chr13:89920145-89920155 chr13:89920145-89920155
25	FOS	chr13:89891680-89892228	MCF10A-Er-Src	breast:	n/a	chr13:89891888-89891900
26	FOS	chr13:89919868-89920566	MCF10A-Er-Src	breast:	n/a	chr13:89920146-89920154 chr13:89920147-89920154 chr13:89920145-89920155 chr13:89920145-89920155 chr13:89920146-89920154 chr13:89920145-89920155 chr13:89920145-89920155
27	FOS	chr13:89919972-89920415	MCF10A-Er-Src	breast:	n/a	chr13:89920146-89920154 chr13:89920147-89920154 chr13:89920145-89920155 chr13:89920145-89920155 chr13:89920146-89920154 chr13:89920145-89920155 chr13:89920145-89920155
28	FOS	chr13:89891634-89892178	MCF10A-Er-Src	breast:	n/a	chr13:89891888-89891900
29	FOS	chr13:89851357-89851651	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr13:89879522-89879998	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr13:89919910-89920581	MCF10A-Er-Src	breast:	n/a	chr13:89920146-89920154 chr13:89920147-89920154 chr13:89920145-89920155 chr13:89920145-89920155 chr13:89920146-89920154 chr13:89920145-89920155 chr13:89920145-89920155
32	FOS	chr13:89879665-89879966	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr13:89918944-89918974	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr13:89879704-89880017	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr13:89851249-89851730	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr13:89891743-89892112	MCF10A-Er-Src	breast:	n/a	chr13:89891888-89891900
37	FOS	chr13:89891662-89892177	MCF10A-Er-Src	breast:	n/a	chr13:89891888-89891900
38	FOXA1	chr13:89864485-89864812	T-47D	breast:	n/a	chr13:89864608-89864623
39	FOXA1	chr13:89864463-89864714	T-47D	breast:	n/a	chr13:89864608-89864623
40	FOXM1	chr13:89856553-89857286	ECC-1	luminal epithelium:	n/a	n/a
41	FOXM1	chr13:89856497-89857158	ECC-1	luminal epithelium:	n/a	n/a
42	FOXP2	chr13:89922042-89922367	SK-N-MC	brain:	n/a	n/a
43	GATA2	chr13:89921979-89922401	SH-SY5Y	brain:	n/a	n/a
44	GATA3	chr13:89922089-89922413	SH-SY5Y	brain:	n/a	n/a
45	GATA3	chr13:89864459-89864800	T-47D	breast:	n/a	chr13:89864633-89864641
46	GATA3	chr13:89879581-89880188	SK-N-SH	brain:	n/a	n/a
47	GATA3	chr13:89885435-89885601	SH-SY5Y	brain:	n/a	n/a
48	GATA3	chr13:89856112-89856312	SH-SY5Y	brain:	n/a	n/a
49	GATA3	chr13:89874429-89874566	SH-SY5Y	brain:	n/a	n/a
50	GATA3	chr13:89864404-89864735	T-47D	breast:	n/a	chr13:89864633-89864641

No.	Distal block	Cell Line	Cell type
1	chr13:89889445..89891378-chr13:89894578..89897231,2	MCF-7	breast:
2	chr13:89889445..89891378-chr13:89894578..89897231,2	MCF-7	breast:
3	chr13:89843854..89844646-chr17:66927017..66927781,2	MCF-7	breast:
4	chr13:89905075..89907672-chr13:89908780..89911039,2	K562	blood:
5	chr13:89905075..89907672-chr13:89908780..89911039,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLITRK6-10	chr13:89867150-89867581	XLOC_010684
2	lnc-SLITRK6-10	chr13:89872788-89872813	XLOC_010684
3	lnc-SLITRK6-10	chr13:89872788-89872813	ENSG00000232225.2
4	lnc-SLITRK6-10	chr13:89889073-89889144	XLOC_010684
5	lnc-SLITRK6-10	chr13:89872788-89872813	ENSG00000232225.2
6	lnc-SLITRK6-10	chr13:89867101-89867581	XLOC_010684
7	lnc-SLITRK6-10	chr13:89870489-89870548	ENSG00000232225.2
8	lnc-SLITRK6-25	chr13:89901072-89902354	NONHSAT034625
9	lnc-SLITRK6-10	chr13:89870489-89870549	XLOC_010684
10	lnc-SLITRK6-10	chr13:89871826-89871963	XLOC_010684
11	lnc-SLITRK6-10	chr13:89870489-89870548	ENSG00000232225.2
12	lnc-SLITRK6-10	chr13:89867150-89867581	ENSG00000232225.2
13	lnc-SLITRK6-10	chr13:89867101-89867581	ENSG00000232225.2
14	lnc-SLITRK6-10	chr13:89870489-89870549	XLOC_010684
15	lnc-SLITRK6-10	chr13:89871825-89871963	ENSG00000232225.2
16	lnc-SLITRK6-10	chr13:89868228-89868395	ENSG00000232225.2
17	lnc-SLITRK6-10	chr13:89889073-89889144	ENSG00000232225.2
18	lnc-SLITRK6-10	chr13:89868228-89868395	XLOC_010684
19	lnc-SLITRK6-10	chr13:89872788-89872813	XLOC_010684

Variant related genes	Relation type
TRIM60P13	TF binding region
LINC00440	TF binding region
LINC01047	TF binding region
RTKN	miRNA target sites
RTN4	miRNA target sites
RTCD1	miRNA target sites
RTF1	miRNA target sites

Extended variants
information (count: 1703 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:1703 , 50 per page) page: 1 2 3 4 5 6 7 ... 35

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs57207757	chr13:89850809-89850810	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs574914185	chr13:89850817-89850818	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs58587355	chr13:89850825-89850826	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs9555857	chr13:89850852-89850853	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs527885801	chr13:89850873-89850874	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs559500857	chr13:89850874-89850875	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs189018728	chr13:89850880-89850881	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs191878506	chr13:89850900-89850901	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs111694221	chr13:89850941-89850942	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs369561665	chr13:89851037-89851038	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs140689338	chr13:89851042-89851043	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs549633274	chr13:89851044-89851045	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs9560248	chr13:89851091-89851092	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs9560249	chr13:89851094-89851095	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs9522457	chr13:89851096-89851097	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs184261835	chr13:89851113-89851114	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs9560250	chr13:89851128-89851129	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs117129877	chr13:89851137-89851138	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs576177554	chr13:89851177-89851178	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs569893531	chr13:89851205-89851206	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs143036562	chr13:89851214-89851215	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs556415666	chr13:89851224-89851225	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs574875697	chr13:89851272-89851273	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs542290836	chr13:89851292-89851293	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs144727329	chr13:89851372-89851373	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs188546051	chr13:89851384-89851385	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs546195784	chr13:89851385-89851386	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs80202942	chr13:89851399-89851400	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs148545555	chr13:89851410-89851411	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs549834509	chr13:89851415-89851416	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs561490232	chr13:89851436-89851437	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs113599774	chr13:89851439-89851440	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs180942310	chr13:89851442-89851443	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs11843359	chr13:89851480-89851481	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs565741177	chr13:89851517-89851518	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs10459312	chr13:89851525-89851526	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs185769034	chr13:89851572-89851573	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs565579501	chr13:89851577-89851578	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs10459313	chr13:89851578-89851579	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs190798118	chr13:89851591-89851592	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs557602731	chr13:89851643-89851644	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs569816496	chr13:89851646-89851647	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs536889554	chr13:89851670-89851671	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs544566475	chr13:89851691-89851692	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs556616348	chr13:89851701-89851702	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs568519771	chr13:89851751-89851752	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs535962505	chr13:89851786-89851787	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs9560251	chr13:89851873-89851874	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs536823805	chr13:89851875-89851876	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs9301544	chr13:89851942-89851943	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
HIV/AIDS	22032296	CNVD
Prostate cancer	16705090	CNVD
High-proliferative meningiomas	17937814	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Chordoma	21602918	CNVD
Bladder cancer	21949216	CNVD
Acute myeloid leukemia	16864856	CNVD
Burkitt''s lymphoma	18698080	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Chronic lymphocytic leukemia	21518781	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Ovarian cancer	20844748	CNVD
Colorectal cancer	19359472	CNVD
Intracranial aneurysm	19064780	CNVD
Breast cancer	19287154	CNVD
Acute myeloid leukemia	18379011	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Multiple myeloma	17077331	CNVD
Ependymoma	16718352	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Myoepithelioma	18604193	CNVD
Breast cancer	17133270	CNVD
Prostate cancer	18632612	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Developmental delay	21147756	CNVD
Melanoma	18172304	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Basal cell lymphoma	17053054	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Metanephric adenoma	20802469	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Gastric cancer	17908304	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Liposarcoma	21253554	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute myeloid leukemia	20729466	CNVD
abnormal development	18461090	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	21965145	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Cancer	21220470	CNVD
Cancer	21183584	CNVD
Omodysplasia	19481194	CNVD
Breast cancer	22032731	CNVD
Mantle cell lymphoma	19690137	CNVD
Rhabdomyosarcoma	17210683	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Medulloblastoma	19270706	CNVD
Myelofibrosis	22110671	CNVD
coloboma	21285886	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	16651412	CNVD
Burkitt''s lymphoma	19759907	CNVD
Wilms tumour	21544195	CNVD

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:89850800-89851200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr13:89850800-89851400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr13:89850800-89851400	Enhancers	HMEC	breast
4	chr13:89850800-89851400	Enhancers	NHEK	skin
5	chr13:89850800-89852400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:89851200-89852200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:89851400-89851800	Flanking Active TSS	NHEK	skin
8	chr13:89851400-89852000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:89851800-89852800	Enhancers	NHEK	skin
10	chr13:89852000-89852200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr13:89852200-89852800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:89852800-89857200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr13:89857200-89858000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr13:89858000-89858600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr13:89858000-89858600	Enhancers	Fetal Lung	lung
16	chr13:89858200-89858600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr13:89860400-89861200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr13:89865800-89867600	Enhancers	Fetal Lung	lung
19	chr13:89866600-89867600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr13:89873400-89875000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:89875000-89890600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:89879600-89880000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr13:89885000-89902400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr13:89890600-89892200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:89890800-89891800	Enhancers	HMEC	breast
26	chr13:89890800-89891800	Enhancers	NHEK	skin
27	chr13:89895400-89896000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr13:89898200-89898600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr13:89898200-89898600	Enhancers	Stomach Mucosa	stomach
30	chr13:89898600-89899600	Weak transcription	Stomach Mucosa	stomach
31	chr13:89899600-89899800	Enhancers	Stomach Mucosa	stomach
32	chr13:89908000-89909000	Enhancers	Fetal Heart	heart
33	chr13:89919800-89920400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr13:89920000-89920400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr13:89920000-89920400	Enhancers	HMEC	breast
36	chr13:89920200-89920400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr13:89920200-89920600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:89920200-89920600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:89920600-89921600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:89921800-89922200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr13:89922200-89922400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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