Variant report

Variant	nsv900853
Chromosome Location	chr13:89824076-89873873
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	chr13:89856664-89857107	ECC-1	luminal epithelium:	n/a	chr13:89856807-89856824
2	CEBPB	chr13:89870206-89870527	HepG2	liver:	n/a	chr13:89870358-89870367 chr13:89870358-89870369 chr13:89870356-89870367
3	CEBPB	chr13:89856691-89857129	ECC-1	luminal epithelium:	n/a	chr13:89856807-89856824
4	CTCF	chr13:89873440-89873590	WERI-Rb-1	eye:	n/a	n/a
5	E2F4	chr13:89856319-89856519	MCF10A-Er-Src	breast:	n/a	n/a
6	E2F4	chr13:89862284-89862740	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F4	chr13:89858454-89858750	MCF10A-Er-Src	breast:	n/a	n/a
8	EP300	chr13:89856582-89857113	ECC-1	luminal epithelium:	n/a	chr13:89856961-89856971
9	EP300	chr13:89856527-89857222	ECC-1	luminal epithelium:	n/a	chr13:89856961-89856971
10	EP300	chr13:89834322-89834358	Hela-S3	cervix:	n/a	n/a
11	FOS	chr13:89851357-89851651	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr13:89851249-89851730	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA1	chr13:89864463-89864714	T-47D	breast:	n/a	chr13:89864608-89864623
14	FOXA1	chr13:89864485-89864812	T-47D	breast:	n/a	chr13:89864608-89864623
15	FOXM1	chr13:89856497-89857158	ECC-1	luminal epithelium:	n/a	n/a
16	FOXM1	chr13:89856553-89857286	ECC-1	luminal epithelium:	n/a	n/a
17	GATA3	chr13:89864459-89864800	T-47D	breast:	n/a	chr13:89864633-89864641
18	GATA3	chr13:89864404-89864735	T-47D	breast:	n/a	chr13:89864633-89864641
19	GATA3	chr13:89856112-89856312	SH-SY5Y	brain:	n/a	n/a
20	JUN	chr13:89857089-89857287	HepG2	liver:	n/a	chr13:89857197-89857210
21	JUND	chr13:89857032-89857301	HepG2	liver:	n/a	n/a
22	JUND	chr13:89867705-89867868	HepG2	liver:	n/a	chr13:89867736-89867747
23	KAP1	chr13:89873637-89874352	HEK293	kidney:	n/a	n/a
24	MAFK	chr13:89851718-89851856	HepG2	liver:	n/a	n/a
25	MAFK	chr13:89853726-89853937	HepG2	liver:	n/a	chr13:89853813-89853830 chr13:89853822-89853833 chr13:89853822-89853833 chr13:89853817-89853832 chr13:89853821-89853832
26	MAFK	chr13:89853756-89853939	HepG2	liver:	n/a	chr13:89853813-89853830 chr13:89853822-89853833 chr13:89853822-89853833 chr13:89853817-89853832 chr13:89853821-89853832
27	MAX	chr13:89858282-89858495	NB4	blood:	n/a	n/a
28	MAZ	chr13:89861231-89861341	HepG2	liver:	n/a	n/a
29	NFIC	chr13:89856547-89857166	ECC-1	luminal epithelium:	n/a	n/a
30	NFYB	chr13:89866289-89866341	GM12878	blood:	n/a	n/a
31	POLR2A	chr13:89833417-89833432	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr13:89858492-89858622	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr13:89850638-89850752	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr13:89870137-89870412	SK-N-MC	brain:	n/a	n/a
35	POLR2A	chr13:89867011-89867052	K562	blood:	n/a	n/a
36	POLR2A	chr13:89859807-89859866	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr13:89868853-89869050	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr13:89866338-89866927	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr13:89864518-89864879	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr13:89851045-89851240	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr13:89857290-89857485	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr13:89831063-89831184	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr13:89852658-89852736	MCF10A-Er-Src	breast:	n/a	n/a
44	RAD21	chr13:89838227-89838477	H1-hESC	embryonic stem cell:	n/a	n/a
45	SETDB1	chr13:89873562-89874441	U2OS	brain:	n/a	n/a
46	SPI1	chr13:89859937-89860313	HL-60	blood:	n/a	chr13:89860091-89860104 chr13:89860095-89860102 chr13:89860094-89860103 chr13:89860092-89860105
47	STAT3	chr13:89840596-89840873	MCF10A-Er-Src	breast:	n/a	n/a
48	STAT3	chr13:89832842-89832864	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT3	chr13:89852995-89853195	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr13:89831051-89831200	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:89843854..89844646-chr17:66927017..66927781,2	MCF-7	breast:

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

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

Extended variants
information (count: 473 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:473 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

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:20 , 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

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