Variant report

Variant	nsv1016477
Chromosome Location	chr5:98922899-98960989
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	CCNT2	chr5:98927320-98927465	K562	blood:	n/a	n/a
2	CEBPB	chr5:98930693-98930960	HepG2	liver:	n/a	chr5:98930825-98930836
3	CEBPB	chr5:98942379-98942440	HepG2	liver:	n/a	chr5:98942416-98942427
4	CEBPB	chr5:98949487-98949659	IMR90	lung:	n/a	chr5:98949503-98949516
5	CEBPB	chr5:98949483-98949681	HepG2	liver:	n/a	chr5:98949503-98949516
6	CEBPB	chr5:98922470-98923076	MCF-7	breast:	n/a	n/a
7	CEBPB	chr5:98922562-98922967	MCF-7	breast:	n/a	n/a
8	CEBPB	chr5:98949448-98949665	A549	lung:	n/a	chr5:98949503-98949516
9	CEBPB	chr5:98926512-98927045	MCF-7	breast:	n/a	n/a
10	CTCF	chr5:98949600-98949750	HRE	kidney:	n/a	n/a
11	CTCF	chr5:98952074-98952106	Lung_OC	lung:	n/a	n/a
12	CTCF	chr5:98934969-98935013	GM13976	blood:	n/a	n/a
13	CTCF	chr5:98956324-98956358	Gliobla	brain:	n/a	n/a
14	E2F4	chr5:98925692-98925865	MCF10A-Er-Src	breast:	n/a	n/a
15	EP300	chr5:98936638-98937043	MCF-7	breast:	n/a	n/a
16	EP300	chr5:98936711-98937117	T-47D	breast:	n/a	n/a
17	EP300	chr5:98942736-98943290	T-47D	breast:	n/a	n/a
18	EP300	chr5:98923774-98923830	GM12878	blood:	n/a	n/a
19	ESR1	chr5:98942903-98943129	T-47D	breast:	n/a	n/a
20	ESR1	chr5:98942881-98943197	T-47D	breast:	n/a	n/a
21	ESR1	chr5:98942860-98943161	T-47D	breast:	n/a	n/a
22	FOS	chr5:98960580-98960700	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr5:98938073-98938250	MCF10A-Er-Src	breast:	n/a	n/a
24	FOSL2	chr5:98926444-98927009	MCF-7	breast:	n/a	n/a
25	FOSL2	chr5:98950591-98950986	MCF-7	breast:	n/a	n/a
26	FOXA1	chr5:98936669-98936962	T-47D	breast:	n/a	n/a
27	FOXA1	chr5:98942818-98943248	T-47D	breast:	n/a	n/a
28	FOXA1	chr5:98950123-98950384	T-47D	breast:	n/a	n/a
29	FOXA1	chr5:98942810-98943256	T-47D	breast:	n/a	n/a
30	FOXA1	chr5:98936703-98937011	T-47D	breast:	n/a	n/a
31	FOXM1	chr5:98926315-98927298	MCF-7	breast:	n/a	n/a
32	GATA2	chr5:98937769-98938164	SH-SY5Y	brain:	n/a	n/a
33	GATA2	chr5:98937518-98938181	HUVEC	blood vessel:	n/a	n/a
34	GATA2	chr5:98936604-98937056	HUVEC	blood vessel:	n/a	n/a
35	GATA3	chr5:98942811-98943248	MCF-7	breast:	n/a	n/a
36	GATA3	chr5:98937531-98938196	MCF-7	breast:	n/a	n/a
37	GATA3	chr5:98936614-98937208	MCF-7	breast:	n/a	n/a
38	GATA3	chr5:98950426-98951139	MCF-7	breast:	n/a	n/a
39	GATA3	chr5:98942773-98943291	T-47D	breast:	n/a	n/a
40	GATA3	chr5:98922236-98923177	MCF-7	breast:	n/a	n/a
41	GATA3	chr5:98942806-98943391	MCF-7	breast:	n/a	n/a
42	GATA3	chr5:98937612-98938055	SK-N-SH	brain:	n/a	n/a
43	GATA3	chr5:98937650-98938104	MCF-7	breast:	n/a	n/a
44	GATA3	chr5:98936416-98938344	MCF-7	breast:	n/a	n/a
45	GATA3	chr5:98937530-98938076	T-47D	breast:	n/a	n/a
46	GATA3	chr5:98936804-98936989	MCF-7	breast:	n/a	n/a
47	GATA3	chr5:98926641-98926988	T-47D	breast:	n/a	chr5:98926766-98926775 chr5:98926766-98926776 chr5:98926768-98926775 chr5:98926945-98926966 chr5:98926768-98926775 chr5:98926768-98926778 chr5:98926768-98926775
48	GATA3	chr5:98926678-98927117	MCF-7	breast:	n/a	chr5:98926766-98926775 chr5:98926766-98926776 chr5:98926768-98926775 chr5:98926945-98926966 chr5:98926768-98926775 chr5:98926768-98926778 chr5:98926768-98926775
49	GATA3	chr5:98950300-98951248	MCF-7	breast:	n/a	n/a
50	GATA3	chr5:98926401-98926991	MCF-7	breast:	n/a	chr5:98926766-98926775 chr5:98926766-98926776 chr5:98926768-98926775 chr5:98926945-98926966 chr5:98926768-98926775 chr5:98926768-98926778 chr5:98926768-98926775

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98936687..98938908-chr5:98939757..98941511,2	MCF-7	breast:
2	chr5:98936687..98938908-chr5:98939757..98941511,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD1-8	chr5:98930033-98930444	NONHSAT102982
2	lnc-RGMB-9	chr5:98930584-98931001	NONHSAT102983

Variant related genes	Relation type
ENSG00000248236	TF binding region
ENSG00000248928	TF binding region

Extended variants
information (count: 713 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:713 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2682158	chr5:98922899-98922900	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs61581123	chr5:98922937-98922938	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs527884870	chr5:98922953-98922954	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs10478060	chr5:98922958-98922959	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs552794321	chr5:98923052-98923053	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs6859856	chr5:98923067-98923068	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs538585692	chr5:98923077-98923078	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs544723038	chr5:98923100-98923101	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs371556520	chr5:98923102-98923103	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs568094922	chr5:98923143-98923144	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs535505617	chr5:98923174-98923175	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs553606424	chr5:98923180-98923181	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs112112609	chr5:98923191-98923192	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs564601602	chr5:98923193-98923194	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs370452574	chr5:98923195-98923196	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs557981464	chr5:98923262-98923263	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs145636436	chr5:98923287-98923288	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs2682157	chr5:98923289-98923290	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs562509657	chr5:98923293-98923294	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs187157204	chr5:98923297-98923298	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs542263349	chr5:98923304-98923305	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs530627919	chr5:98923312-98923313	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs201888224	chr5:98923332-98923333	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs560391218	chr5:98923339-98923340	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs60406906	chr5:98923345-98923346	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs78222739	chr5:98923348-98923349	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs6861784	chr5:98923389-98923390	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs555918888	chr5:98923391-98923392	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs200866294	chr5:98923405-98923406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs6861804	chr5:98923419-98923420	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs550508718	chr5:98923431-98923432	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs568032443	chr5:98923469-98923470	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs566970857	chr5:98923515-98923516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs191541439	chr5:98923516-98923517	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs553772369	chr5:98923598-98923599	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs2682156	chr5:98923665-98923666	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs183181628	chr5:98923673-98923674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs557516799	chr5:98923684-98923685	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs76318667	chr5:98923688-98923689	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs78279105	chr5:98923689-98923690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs78527256	chr5:98923690-98923691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs398050590	chr5:98923700-98923701	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs575848037	chr5:98923754-98923755	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs536920391	chr5:98923787-98923788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs555247359	chr5:98923800-98923801	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs75130761	chr5:98923884-98923885	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs541848361	chr5:98923894-98923895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs560579660	chr5:98923937-98923938	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs75950326	chr5:98923955-98923956	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs546312180	chr5:98923974-98923975	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Cancer	16751803	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
Non-small cell lung cancer	21829676	CNVD
adenomatous polyposis	22470819	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Urothelial carcinoma	21177765	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
Lung cancer	18438408	CNVD
Retinoblastoma	22278416	CNVD
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
Breast cancer	21785460	CNVD
Merkel cell carcinoma	19020549	CNVD
Squamous cell cancer	20885788	CNVD
Hepatocellular carcinoma	16750200	CNVD
Neurodevelopmental disorder	22521361	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	17133270	CNVD
Acute myeloid leukemia	20729466	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
lymphocytic leukemia	21291569	CNVD
Testicular cancer	18059402	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16573809	CNVD
Renal cell carcinoma	18194544	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Cancer	20164920	CNVD
Myelodysplastic syndrome	21251322	CNVD
abnormal development	18461090	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16774939	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Multiple myeloma	17550852	CNVD
Glioblastoma multiforme	22286061	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Ovarian cancer	21720365	CNVD
Prostate cancer	16461572	CNVD
Neurocytoma	17123091	CNVD
Salivary gland tumor	18059337	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98915200-98930800	Weak transcription	Fetal Heart	heart
2	chr5:98922200-98923000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:98922800-98923400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:98930800-98931800	Enhancers	Fetal Heart	heart
5	chr5:98931800-98932000	Flanking Active TSS	Fetal Heart	heart
6	chr5:98932000-98932200	Enhancers	Fetal Heart	heart
7	chr5:98932200-98932400	Flanking Active TSS	Fetal Heart	heart
8	chr5:98932400-98932600	Enhancers	Fetal Heart	heart
9	chr5:98936600-98937200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:98936600-98937800	Enhancers	HUVEC	blood vessel
11	chr5:98936600-98938200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:98937200-98937600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:98937200-98937600	Enhancers	Dnd41	blood
14	chr5:98937400-98938000	Enhancers	Adipose Nuclei	Adipose
15	chr5:98937600-98938000	Flanking Active TSS	Dnd41	blood
16	chr5:98937800-98938000	Enhancers	Pancreas	Pancrea
17	chr5:98938000-98938200	Enhancers	Dnd41	blood
18	chr5:98939400-98946400	Weak transcription	Pancreas	Pancrea
19	chr5:98950600-98951200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:98950800-98951200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:98957600-98958000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:98957800-98958200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:98957800-98958200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:98957800-98958400	Enhancers	H1 Cell Line	embryonic stem cell
25	chr5:98958000-98958400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:98958000-98958600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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