Variant report

Variant	nsv879048
Chromosome Location	chr4:60053789-60512343
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	ATF1	chr4:60234853-60235081	K562	blood:	n/a	n/a
2	ATF2	chr4:60419115-60419467	GM12878	blood:	n/a	n/a
3	BACH1	chr4:60182367-60182421	H1-hESC	embryonic stem cell:	n/a	n/a
4	BATF	chr4:60439526-60439802	GM12878	blood:	n/a	n/a
5	BATF	chr4:60419091-60419374	GM12878	blood:	n/a	n/a
6	BATF	chr4:60419100-60419406	GM12878	blood:	n/a	n/a
7	BATF	chr4:60401319-60401538	GM12878	blood:	n/a	chr4:60401429-60401440
8	BATF	chr4:60401251-60401624	GM12878	blood:	n/a	chr4:60401429-60401440
9	BATF	chr4:60436963-60437115	GM12878	blood:	n/a	n/a
10	BATF	chr4:60439519-60439795	GM12878	blood:	n/a	n/a
11	BCL11A	chr4:60401311-60401576	GM12878	blood:	n/a	n/a
12	BCL11A	chr4:60419048-60419387	GM12878	blood:	n/a	n/a
13	BHLHE40	chr4:60419045-60419363	GM12878	blood:	n/a	n/a
14	BHLHE40	chr4:60401391-60401591	GM12878	blood:	n/a	n/a
15	BRCA1	chr4:60214669-60214729	H1-hESC	embryonic stem cell:	n/a	n/a
16	BRCA1	chr4:60432414-60432580	Hela-S3	cervix:	n/a	n/a
17	BRCA1	chr4:60249612-60249626	H1-hESC	embryonic stem cell:	n/a	n/a
18	BRCA1	chr4:60377596-60377875	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr4:60084012-60084308	Hela-S3	cervix:	n/a	chr4:60084162-60084171 chr4:60084162-60084171 chr4:60084160-60084171 chr4:60084162-60084171
20	CEBPB	chr4:60083993-60084328	IMR90	lung:	n/a	chr4:60084162-60084171 chr4:60084162-60084171 chr4:60084160-60084171 chr4:60084162-60084171
21	CEBPB	chr4:60264068-60264350	HepG2	liver:	n/a	chr4:60264207-60264218
22	CEBPB	chr4:60388595-60389160	HepG2	liver:	n/a	chr4:60389093-60389104
23	CEBPB	chr4:60404866-60405095	IMR90	lung:	n/a	chr4:60404995-60405006
24	CEBPB	chr4:60404855-60405120	HepG2	liver:	n/a	chr4:60404995-60405006
25	CEBPB	chr4:60084598-60084895	HepG2	liver:	n/a	chr4:60084724-60084735 chr4:60084725-60084736 chr4:60084726-60084735
26	CEBPB	chr4:60477990-60478363	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr4:60066746-60067053	HepG2	liver:	n/a	chr4:60066902-60066915 chr4:60066902-60066913 chr4:60066904-60066915
28	CEBPB	chr4:60083977-60084319	K562	blood:	n/a	chr4:60084162-60084171 chr4:60084162-60084171 chr4:60084160-60084171 chr4:60084162-60084171
29	CEBPB	chr4:60383198-60383449	HepG2	liver:	n/a	chr4:60383336-60383347
30	CEBPB	chr4:60426929-60427254	IMR90	lung:	n/a	chr4:60427091-60427104 chr4:60427091-60427102
31	CEBPB	chr4:60069581-60069860	A549	lung:	n/a	chr4:60069699-60069710
32	CEBPB	chr4:60119455-60119745	IMR90	lung:	n/a	chr4:60119596-60119609 chr4:60119596-60119607
33	CEBPB	chr4:60066672-60067062	MCF-7	breast:	n/a	chr4:60066902-60066915 chr4:60066902-60066913 chr4:60066904-60066915
34	CEBPB	chr4:60150403-60150678	HepG2	liver:	n/a	chr4:60150512-60150523
35	CEBPB	chr4:60136450-60136711	A549	lung:	n/a	chr4:60136580-60136591 chr4:60136581-60136592
36	CEBPB	chr4:60083977-60084303	A549	lung:	n/a	chr4:60084162-60084171 chr4:60084162-60084171 chr4:60084160-60084171 chr4:60084162-60084171
37	CEBPB	chr4:60461172-60461394	IMR90	lung:	n/a	n/a
38	CEBPB	chr4:60264042-60264310	Hela-S3	cervix:	n/a	chr4:60264207-60264218
39	CEBPB	chr4:60136409-60136731	IMR90	lung:	n/a	chr4:60136580-60136591 chr4:60136581-60136592
40	CEBPB	chr4:60463619-60463920	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr4:60083979-60084344	HepG2	liver:	n/a	chr4:60084162-60084171 chr4:60084162-60084171 chr4:60084160-60084171 chr4:60084162-60084171
42	CEBPB	chr4:60511865-60512111	HepG2	liver:	n/a	n/a
43	CEBPB	chr4:60371676-60371876	HepG2	liver:	n/a	n/a
44	CEBPB	chr4:60066644-60067058	MCF-7	breast:	n/a	chr4:60066902-60066915 chr4:60066902-60066913 chr4:60066904-60066915
45	CEBPB	chr4:60426929-60427274	HepG2	liver:	n/a	chr4:60427091-60427104 chr4:60427091-60427102
46	CEBPB	chr4:60119487-60119727	HepG2	liver:	n/a	chr4:60119596-60119609 chr4:60119596-60119607
47	CEBPB	chr4:60383229-60383460	A549	lung:	n/a	chr4:60383336-60383347
48	CEBPB	chr4:60069680-60069873	HepG2	liver:	n/a	chr4:60069699-60069710
49	CEBPB	chr4:60131394-60131635	HepG2	liver:	n/a	chr4:60131460-60131471
50	CEBPB	chr4:60136456-60136735	HepG2	liver:	n/a	chr4:60136580-60136591 chr4:60136581-60136592

No.	Distal block	Cell Line	Cell type
1	chr4:60276368..60277207-chr6:157803055..157803704,2	MCF-7	breast:
2	chr4:60124718..60127402-chr4:60132067..60134708,2	K562	blood:
3	chr14:63626389..63627074-chr4:60415889..60416567,2	MCF-7	breast:
4	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:
5	chr4:60079114..60081147-chr4:60084061..60086552,2	MCF-7	breast:
6	chr4:60301296..60303463-chr4:60317465..60318968,2	K562	blood:
7	chr4:60112476..60113371-chr4:61066907..61067441,2	K562	blood:
8	chr4:60478745..60481440-chr4:60481767..60484414,3	MCF-7	breast:
9	chr4:60079114..60081147-chr4:60084061..60086552,2	MCF-7	breast:
10	chr4:60301296..60303463-chr4:60317465..60318968,2	K562	blood:
11	chr4:60124718..60127402-chr4:60132067..60134708,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IGFBP7-7	chr4:60429941-60430063	XLOC_003964
2	lnc-IGFBP7-7	chr4:60426719-60426805	XLOC_003964
3	lnc-IGFBP7-7	chr4:60460138-60460197	XLOC_003964
4	lnc-IGFBP7-7	chr4:60416860-60416972	XLOC_003964
5	lnc-IGFBP7-7	chr4:60495929-60496042	XLOC_003964
6	lnc-IGFBP7-7	chr4:60440016-60440076	XLOC_003964

Variant related genes	Relation type
ENSG00000249392	TF binding region
ENSG00000199780	TF binding region
RUNX2	miRNA target sites

Extended variants
information (count: 5777 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:5777 , 50 per page) page: 1 2 3 4 5 6 7 ... 116

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs569926245	chr4:60060406-60060407	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs149806701	chr4:60060426-60060427	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs145760778	chr4:60060430-60060431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs577698212	chr4:60060471-60060472	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs544763859	chr4:60060508-60060509	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs553772339	chr4:60060510-60060511	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs10001575	chr4:60060520-60060521	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs542908068	chr4:60060532-60060533	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs561123846	chr4:60060540-60060541	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs148940147	chr4:60060587-60060588	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs568084685	chr4:60060590-60060591	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs7672870	chr4:60060600-60060601	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs565051813	chr4:60060628-60060629	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs188184794	chr4:60060633-60060634	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs7691310	chr4:60060662-60060663	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs566070307	chr4:60060679-60060680	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs7691338	chr4:60060730-60060731	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs560845596	chr4:60060733-60060734	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs569986855	chr4:60060759-60060760	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs7664607	chr4:60060761-60060762	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs558762726	chr4:60060780-60060781	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs147024996	chr4:60060785-60060786	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs538775208	chr4:60060789-60060790	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs12503764	chr4:60060840-60060841	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs192573105	chr4:60060841-60060842	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs7696174	chr4:60060870-60060871	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs536173313	chr4:60060882-60060883	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs570840007	chr4:60060906-60060907	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs545884201	chr4:60060924-60060925	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs554922288	chr4:60060941-60060942	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs200178174	chr4:60060999-60061000	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs147641659	chr4:60061042-60061043	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs7696570	chr4:60061066-60061067	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs142241399	chr4:60061077-60061078	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs7665625	chr4:60061258-60061259	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs145983229	chr4:60061288-60061289	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs559554795	chr4:60061295-60061296	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs112370553	chr4:60061340-60061341	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs185593170	chr4:60061347-60061348	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs73200564	chr4:60061357-60061358	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs531152212	chr4:60061365-60061366	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs552450294	chr4:60061385-60061386	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs73200567	chr4:60061473-60061474	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs541907968	chr4:60061476-60061477	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs534863126	chr4:60061541-60061542	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs10007636	chr4:60061549-60061550	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs565607567	chr4:60061551-60061552	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs370342781	chr4:60061558-60061559	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs372341314	chr4:60061600-60061601	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs190166592	chr4:60061652-60061653	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Multiple myeloma	16616336	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Colorectal cancer	16272173	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute monocytic leukemia	16498392	CNVD
Prostate cancer	16573809	CNVD
Osteoporosis	18992858	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	20369283	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:333 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:60060400-60062400	Enhancers	Fetal Heart	heart
2	chr4:60061800-60062200	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr4:60062400-60065600	Weak transcription	Fetal Heart	heart
4	chr4:60065600-60067600	Enhancers	Fetal Heart	heart
5	chr4:60066000-60067200	Enhancers	Adipose Nuclei	Adipose
6	chr4:60066400-60066800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:60066400-60066800	Enhancers	Aorta	Aorta
8	chr4:60066400-60066800	Enhancers	Stomach Smooth Muscle	stomach
9	chr4:60066800-60067600	Active TSS	Aorta	Aorta
10	chr4:60070800-60072200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:60072200-60072400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr4:60072200-60072400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:60077000-60078800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:60078800-60079000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:60090600-60091000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:60103800-60104000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:60103800-60104200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:60104000-60109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:60104600-60104800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr4:60104600-60105000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:60104600-60105000	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr4:60104800-60105000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr4:60105000-60105400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:60105000-60105400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:60105000-60105800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:60105000-60106000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:60105400-60106400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:60105400-60107000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr4:60105600-60106400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:60105800-60106000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr4:60105800-60106400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:60106000-60106600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr4:60106000-60107000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:60107000-60107200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr4:60108800-60109400	Enhancers	Dnd41	blood
36	chr4:60109000-60109200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:60110600-60111000	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr4:60113200-60114000	Enhancers	Liver	Liver
39	chr4:60114000-60114600	Flanking Active TSS	Liver	Liver
40	chr4:60114600-60115000	Enhancers	Liver	Liver
41	chr4:60122400-60123000	Enhancers	Fetal Heart	heart
42	chr4:60158800-60159000	Enhancers	Pancreas	Pancrea
43	chr4:60168800-60169000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
44	chr4:60168800-60169000	ZNF genes & repeats	Colon Smooth Muscle	Colon
45	chr4:60168800-60169000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
46	chr4:60169000-60174600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:60174600-60175000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:60174600-60175000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr4:60174600-60175000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr4:60174600-60175000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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