Variant report

Variant	nsv1012297
Chromosome Location	chr3:592390-729489
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	BATF	chr3:638972-639242	GM12878	blood:	n/a	chr3:639093-639102
2	BATF	chr3:599827-600084	GM12878	blood:	n/a	chr3:599953-599962
3	BATF	chr3:599789-600089	GM12878	blood:	n/a	chr3:599953-599962
4	BCLAF1	chr3:599656-600200	GM12878	blood:	n/a	chr3:599779-599788 chr3:599826-599835
5	BRCA1	chr3:674381-674581	H1-hESC	embryonic stem cell:	n/a	n/a
6	BRCA1	chr3:638578-639330	Hela-S3	cervix:	n/a	n/a
7	BRCA1	chr3:639591-639851	Hela-S3	cervix:	n/a	n/a
8	BRCA1	chr3:649451-649478	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr3:638934-639824	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr3:649124-649464	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr3:700961-701300	Hela-S3	cervix:	n/a	chr3:701126-701139 chr3:701128-701137 chr3:701128-701137 chr3:701128-701137
12	CEBPB	chr3:611097-611344	HepG2	liver:	n/a	chr3:611201-611212
13	CEBPB	chr3:697395-697928	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr3:700997-701241	H1-hESC	embryonic stem cell:	n/a	chr3:701126-701139 chr3:701128-701137 chr3:701128-701137 chr3:701128-701137
15	CEBPB	chr3:672472-672697	A549	lung:	n/a	chr3:672554-672567 chr3:672555-672566
16	CEBPB	chr3:700968-701307	HepG2	liver:	n/a	chr3:701126-701139 chr3:701128-701137 chr3:701128-701137 chr3:701128-701137
17	CEBPB	chr3:637765-638119	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr3:650024-650224	A549	lung:	n/a	chr3:650073-650084 chr3:650075-650084
19	CEBPB	chr3:672488-672700	HepG2	liver:	n/a	chr3:672554-672567 chr3:672555-672566
20	CEBPB	chr3:674328-674574	H1-hESC	embryonic stem cell:	n/a	n/a
21	CEBPB	chr3:650039-650244	HepG2	liver:	n/a	chr3:650073-650084 chr3:650075-650084
22	CEBPB	chr3:649955-650248	IMR90	lung:	n/a	chr3:650073-650084 chr3:650075-650084
23	CEBPB	chr3:701078-701278	A549	lung:	n/a	chr3:701126-701139 chr3:701128-701137 chr3:701128-701137 chr3:701128-701137
24	CEBPB	chr3:700965-701296	IMR90	lung:	n/a	chr3:701126-701139 chr3:701128-701137 chr3:701128-701137 chr3:701128-701137
25	CHD1	chr3:660628-660658	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD2	chr3:639101-639345	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr3:674360-674510	HPF	lung:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
28	CTCF	chr3:674360-674510	HCPEpiC	choroid plexus:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
29	CTCF	chr3:616940-617090	HepG2	liver:	n/a	n/a
30	CTCF	chr3:674340-674490	HFF-Myc	foreskin:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
31	CTCF	chr3:674400-674550	HepG2	liver:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
32	CTCF	chr3:674246-674596	H1-hESC	embryonic stem cell:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
33	CTCF	chr3:674360-674510	GM12869	blood:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
34	CTCF	chr3:674380-674530	GM12873	blood:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
35	CTCF	chr3:674231-674676	GM12878	blood:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
36	CTCF	chr3:615631-615719	ProgFib	skin:	n/a	n/a
37	CTCF	chr3:674400-674550	SAEC	small airway:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
38	CTCF	chr3:674341-674569	HepG2	liver:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
39	CTCF	chr3:674303-674569	HepG2	liver:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
40	CTCF	chr3:616940-617090	A549	lung:	n/a	n/a
41	CTCF	chr3:674400-674550	GM12873	blood:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
42	CTCF	chr3:674309-674584	GM13977	blood:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
43	CTCF	chr3:674380-674530	HUVEC	blood vessel:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
44	CTCF	chr3:674337-674560	NHEK	skin:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
45	CTCF	chr3:674400-674550	HFF	foreskin:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
46	CTCF	chr3:608164-608208	GM20000	blood:	n/a	n/a
47	CTCF	chr3:674020-674170	GM12864	blood:	n/a	n/a
48	CTCF	chr3:674372-674546	A549	lung:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473
49	CTCF	chr3:676240-676390	HBMEC	blood vessel:	n/a	n/a
50	CTCF	chr3:674357-674549	GM19239	blood:	n/a	chr3:674455-674465 chr3:674451-674467 chr3:674453-674466 chr3:674453-674462 chr3:674453-674466 chr3:674450-674468 chr3:674452-674473

No.	Distal block	Cell Line	Cell type
1	chr3:674217..674800-chr3:1123463..1123990,2	MCF-7	breast:
2	chr21:9517250..9519290-chr3:632442..635070,2	MCF-7	breast:
3	chr3:703062..705164-chr3:828470..830008,2	K562	blood:
4	chr3:709932..711493-chr3:712317..715172,2	K562	blood:
5	chr3:522873..523625-chr3:674344..674995,2	MCF-7	breast:
6	chr3:674203..674975-chr3:2197712..2198482,2	MCF-7	breast:
7	chr3:726576..727076-chr3:11025934..11026463,2	MCF-7	breast:
8	chr3:709932..711493-chr3:712317..715172,2	K562	blood:
9	chr21:9537493..9539688-chr3:612236..614804,2	MCF-7	breast:
10	chr21:9533639..9536328-chr3:614645..617390,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL5RA-14	chr3:659472-659997	NONHSAT087571
2	lnc-CHL1-3	chr3:633788-633866	NR_110118
3	lnc-CHL1-6	chr3:608788-608866	ucscGeneNc_uc003boy_1
4	lnc-CHL1-3	chr3:633788-633866	ENSG00000224957

Variant related genes	Relation type
ENSG00000238075	TF binding region
DCBLD2	miRNA target sites

Extended variants
information (count: 1809 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:1809 , 50 per page) page: 1 2 3 4 5 6 7 ... 37

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs533746462	chr3:592429-592430	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs143097702	chr3:592440-592441	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs375964803	chr3:592459-592460	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs181816914	chr3:592472-592473	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs114385256	chr3:592482-592483	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs377753913	chr3:592509-592510	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs575900208	chr3:592516-592517	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs539781258	chr3:592519-592520	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs558025516	chr3:592579-592580	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs572938527	chr3:592599-592600	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs554893836	chr3:592651-592652	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs532609505	chr3:592659-592660	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs539481179	chr3:592673-592674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs113572771	chr3:592714-592715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs199600770	chr3:592733-592734	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs547208990	chr3:592761-592762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs77019198	chr3:592762-592763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs75193129	chr3:592763-592764	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs540201929	chr3:592766-592767	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs562233383	chr3:592772-592773	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs78147491	chr3:592773-592774	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs574004508	chr3:592776-592777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs547594395	chr3:592874-592875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs186387343	chr3:592891-592892	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs10663053	chr3:592904-592905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs67298197	chr3:592905-592906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs80344013	chr3:592908-592909	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs72991441	chr3:592985-592986	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs189579228	chr3:592988-592989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs370218354	chr3:593076-593077	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs148214229	chr3:593109-593110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs180850736	chr3:593174-593175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs551728936	chr3:593211-593212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs186248260	chr3:593219-593220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs533800185	chr3:593247-593248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs527297551	chr3:593301-593302	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs191021469	chr3:593326-593327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs141161685	chr3:593335-593336	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs537502190	chr3:593339-593340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs549838325	chr3:593358-593359	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs368025101	chr3:593361-593362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs539631417	chr3:593364-593365	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs371959659	chr3:593383-593384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs558046338	chr3:593394-593395	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs566796951	chr3:593405-593406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs534202763	chr3:593415-593416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs570068608	chr3:593416-593417	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs558559767	chr3:593417-593418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs537522090	chr3:593453-593454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs371115912	chr3:593454-593455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:589800-592600	Enhancers	Hela-S3	cervix
2	chr3:590600-594400	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:590600-595600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:592600-593800	Weak transcription	Hela-S3	cervix
5	chr3:593800-595000	Enhancers	Hela-S3	cervix
6	chr3:594400-594600	Enhancers	Aorta	Aorta
7	chr3:594400-597200	Strong transcription	Fetal Muscle Leg	muscle
8	chr3:594600-607600	Weak transcription	Aorta	Aorta
9	chr3:595600-597000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr3:597000-598600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:597200-602600	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:599200-599400	Enhancers	GM12878-XiMat	blood
13	chr3:599400-599800	Flanking Active TSS	GM12878-XiMat	blood
14	chr3:599800-600600	Enhancers	GM12878-XiMat	blood
15	chr3:602600-603200	Enhancers	Fetal Muscle Leg	muscle
16	chr3:602800-603000	Enhancers	Fetal Brain Male	brain
17	chr3:603000-606000	Weak transcription	Fetal Brain Male	brain
18	chr3:603200-603400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:606000-607000	Enhancers	Fetal Brain Male	brain
20	chr3:607000-610000	Weak transcription	Fetal Brain Male	brain
21	chr3:607600-608400	Enhancers	Aorta	Aorta
22	chr3:608800-610600	Enhancers	Brain Germinal Matrix	brain
23	chr3:610000-611200	Enhancers	Fetal Brain Male	brain
24	chr3:610200-610600	Enhancers	Ovary	ovary
25	chr3:611200-612400	Weak transcription	Fetal Brain Male	brain
26	chr3:612600-612800	Enhancers	Fetal Brain Male	brain
27	chr3:636400-642600	Enhancers	Hela-S3	cervix
28	chr3:639200-639800	Enhancers	Dnd41	blood
29	chr3:649000-650000	Enhancers	Hela-S3	cervix
30	chr3:649200-650200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:659600-660000	Active TSS	Spleen	Spleen
32	chr3:663600-664000	Enhancers	Fetal Brain Male	brain
33	chr3:674200-674800	Enhancers	Brain Substantia Nigra	brain
34	chr3:674200-675000	Enhancers	Hela-S3	cervix
35	chr3:675800-676400	Enhancers	Fetal Thymus	thymus
36	chr3:682800-683200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:684800-685200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:697200-697600	Enhancers	Hela-S3	cervix
39	chr3:703200-703400	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr3:703400-703800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:706200-708000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:715600-716600	Enhancers	Fetal Brain Male	brain
43	chr3:716600-717800	Weak transcription	Fetal Brain Male	brain
44	chr3:718000-718200	Enhancers	Fetal Brain Male	brain
45	chr3:722800-723800	Enhancers	Hela-S3	cervix
46	chr3:723800-724400	Weak transcription	Hela-S3	cervix
47	chr3:724400-724600	Enhancers	Hela-S3	cervix
48	chr3:727000-727200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:729000-729400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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