Variant report

Variant	nsv460482
Chromosome Location	chr3:24966768-25071616
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	ATF2	chr3:24993812-24994233	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF2	chr3:24993855-24994300	H1-hESC	embryonic stem cell:	n/a	n/a
3	BATF	chr3:25049457-25049847	GM12878	blood:	n/a	chr3:25049644-25049654 chr3:25049643-25049654
4	BATF	chr3:25049508-25049846	GM12878	blood:	n/a	chr3:25049644-25049654 chr3:25049643-25049654
5	BRCA1	chr3:25057869-25057895	GM12878	blood:	n/a	n/a
6	CEBPB	chr3:25063291-25063740	MCF-7	breast:	n/a	n/a
7	CEBPB	chr3:25047856-25048221	HepG2	liver:	n/a	chr3:25048029-25048040 chr3:25048132-25048144 chr3:25048026-25048043
8	CEBPB	chr3:25063335-25063656	HCT-116	colon:	n/a	n/a
9	CEBPB	chr3:25002367-25002493	HepG2	liver:	n/a	chr3:25002420-25002431 chr3:25002419-25002432
10	CEBPB	chr3:25063355-25063683	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr3:25002702-25002970	A549	lung:	n/a	chr3:25002818-25002831 chr3:25002820-25002829 chr3:25002820-25002829 chr3:25002819-25002830 chr3:25002820-25002829 chr3:25002820-25002829 chr3:25002818-25002831 chr3:25002818-25002829
12	CEBPB	chr3:25047896-25048169	K562	blood:	n/a	chr3:25048029-25048040 chr3:25048132-25048144 chr3:25048026-25048043
13	CEBPB	chr3:25007189-25007775	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr3:25043943-25044158	HepG2	liver:	n/a	chr3:25044068-25044077 chr3:25044068-25044077 chr3:25044068-25044077
15	CEBPB	chr3:25063341-25063696	H1-hESC	embryonic stem cell:	n/a	n/a
16	CEBPB	chr3:25007267-25007482	A549	lung:	n/a	n/a
17	CEBPB	chr3:25047888-25048176	A549	lung:	n/a	chr3:25048029-25048040 chr3:25048132-25048144 chr3:25048026-25048043
18	CEBPB	chr3:25063424-25063689	A549	lung:	n/a	n/a
19	CEBPB	chr3:25063337-25063695	A549	lung:	n/a	n/a
20	CEBPB	chr3:25043924-25044206	H1-hESC	embryonic stem cell:	n/a	chr3:25044068-25044077 chr3:25044068-25044077 chr3:25044068-25044077
21	CEBPB	chr3:25038559-25038810	HepG2	liver:	n/a	n/a
22	CEBPB	chr3:25047919-25048119	H1-hESC	embryonic stem cell:	n/a	chr3:25048029-25048040 chr3:25048026-25048043
23	CEBPB	chr3:25024507-25024824	IMR90	lung:	n/a	chr3:25024669-25024680
24	CEBPB	chr3:25063369-25063663	HepG2	liver:	n/a	n/a
25	CEBPB	chr3:25047884-25048211	IMR90	lung:	n/a	chr3:25048029-25048040 chr3:25048132-25048144 chr3:25048026-25048043
26	CEBPB	chr3:25043902-25044137	A549	lung:	n/a	chr3:25044068-25044077 chr3:25044068-25044077 chr3:25044068-25044077
27	CEBPB	chr3:25043936-25044191	K562	blood:	n/a	chr3:25044068-25044077 chr3:25044068-25044077 chr3:25044068-25044077
28	CEBPB	chr3:25063283-25063734	MCF-7	breast:	n/a	n/a
29	CEBPB	chr3:25002688-25002888	K562	blood:	n/a	chr3:25002818-25002831 chr3:25002820-25002829 chr3:25002820-25002829 chr3:25002819-25002830 chr3:25002820-25002829 chr3:25002820-25002829 chr3:25002818-25002831 chr3:25002818-25002829
30	CEBPB	chr3:25032982-25033296	HepG2	liver:	n/a	chr3:25033112-25033123
31	CEBPB	chr3:25063204-25063740	A549	lung:	n/a	n/a
32	CEBPB	chr3:25024512-25024830	HepG2	liver:	n/a	chr3:25024669-25024680
33	CEBPB	chr3:25024625-25024753	H1-hESC	embryonic stem cell:	n/a	chr3:25024669-25024680
34	CEBPB	chr3:25063422-25063554	K562	blood:	n/a	n/a
35	CEBPB	chr3:25024533-25024818	A549	lung:	n/a	chr3:25024669-25024680
36	CEBPB	chr3:25024582-25024801	Hela-S3	cervix:	n/a	chr3:25024669-25024680
37	CEBPB	chr3:25048670-25048717	H1-hESC	embryonic stem cell:	n/a	n/a
38	CEBPB	chr3:25033111-25033197	A549	lung:	n/a	chr3:25033112-25033123
39	CEBPB	chr3:25043904-25044225	IMR90	lung:	n/a	chr3:25044068-25044077 chr3:25044068-25044077 chr3:25044068-25044077
40	CEBPB	chr3:25002724-25002997	HepG2	liver:	n/a	chr3:25002818-25002831 chr3:25002820-25002829 chr3:25002820-25002829 chr3:25002819-25002830 chr3:25002820-25002829 chr3:25002820-25002829 chr3:25002818-25002831 chr3:25002818-25002829
41	CEBPB	chr3:24992882-24993031	HepG2	liver:	n/a	n/a
42	CHD2	chr3:24993862-24994292	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr3:25005380-25005530	Hela-S3	cervix:	n/a	chr3:25005452-25005470
44	CTCF	chr3:25005326-25005562	A549	lung:	n/a	chr3:25005452-25005470
45	CTCF	chr3:25005420-25005570	AG04450	lung:	n/a	chr3:25005452-25005470
46	CTCF	chr3:25063340-25063490	A549	lung:	n/a	n/a
47	CTCF	chr3:25005280-25005430	A549	lung:	n/a	n/a
48	CTCF	chr3:25063380-25063530	GM12865	blood:	n/a	n/a
49	CTCF	chr3:25005380-25005530	AG04449	skin:	n/a	chr3:25005452-25005470
50	CTCF	chr3:25063460-25063610	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:25063013..25063625-chr3:25635402..25636430,4	MCF-7	breast:
2	chr16:69106267..69106856-chr3:25010489..25010989,2	HCT-116	colon:
3	chr3:25063074..25063594-chr3:25635286..25636033,2	MCF-7	breast:
4	chr3:25053220..25055961-chr3:25057808..25059826,2	K562	blood:
5	chr3:24980900..24983100-chr3:24983885..24986505,2	K562	blood:
6	chr3:24984996..24987861-chr3:24992367..24994337,2	K562	blood:
7	chr3:24980900..24983100-chr3:24983885..24986505,2	K562	blood:
8	chr3:25014243..25016013-chr3:25025962..25028034,2	K562	blood:
9	chr3:24971555..24974140-chr3:26540634..26543140,2	K562	blood:
10	chr3:25005007..25005513-chr3:25136423..25137233,2	MCF-7	breast:
11	chr3:25032348..25035349-chr3:25037207..25041115,3	MCF-7	breast:
12	chr3:24993898..24995691-chr3:25054784..25056351,2	K562	blood:
13	chr3:24984996..24987861-chr3:24992367..24994337,2	K562	blood:
14	chr3:25014243..25016013-chr3:25025962..25028034,2	K562	blood:
15	chr3:25005071..25005603-chr3:25074628..25075570,3	MCF-7	breast:
16	chr3:24999490..25001286-chr3:25005454..25007613,2	K562	blood:
17	chr3:24993898..24995691-chr3:25054784..25056351,2	K562	blood:
18	chr3:25039709..25042401-chr3:25047247..25049664,2	K562	blood:
19	chr3:24976191..24978816-chr3:24982389..24985346,2	K562	blood:
20	chr3:25032348..25035349-chr3:25037207..25041115,3	MCF-7	breast:
21	chr3:25012469..25014834-chr3:25636551..25638421,2	MCF-7	breast:
22	chr3:24999490..25001286-chr3:25005454..25007613,2	K562	blood:
23	chr3:25039709..25042401-chr3:25047247..25049664,2	K562	blood:
24	chr3:24976922..24979133-chr3:24980723..24982726,2	K562	blood:
25	chr3:24975006..24977097-chr3:24999784..25002405,2	K562	blood:
26	chr3:24976191..24978816-chr3:24982389..24985346,2	K562	blood:
27	chr3:24815127..24815890-chr3:25004964..25005522,2	MCF-7	breast:
28	chr3:25062997..25063972-chr3:25074606..25075214,3	MCF-7	breast:
29	chr3:25053220..25055961-chr3:25057808..25059826,2	K562	blood:
30	chr3:25063071..25063645-chr3:25482470..25483148,2	MCF-7	breast:
31	chr3:24976922..24979133-chr3:24980723..24982726,2	K562	blood:
32	chr3:24975006..24977097-chr3:24999784..25002405,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THRB-5	chr3:25061654-25061954	NONHSAT088706

Variant related genes	Relation type
RN7SL216P	TF binding region
RNA5SP125	TF binding region
ENSG00000229421	chromatin interactions

Extended variants
information (count: 3689 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:3689 , 50 per page) page: 1 2 3 4 5 6 7 ... 74

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10510553	chr3:24966768-24966769	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs146887219	chr3:24966786-24966787	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs529844059	chr3:24966800-24966801	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs574870006	chr3:24966814-24966815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs17015464	chr3:24966831-24966832	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs140649798	chr3:24966834-24966835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs113425158	chr3:24966835-24966836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs546529975	chr3:24966859-24966860	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs564823158	chr3:24966910-24966911	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs150460463	chr3:24966916-24966917	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs190552579	chr3:24966951-24966952	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs75449980	chr3:24966971-24966972	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs529781501	chr3:24966979-24966980	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs549922277	chr3:24967006-24967007	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs9310765	chr3:24967044-24967045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs566259008	chr3:24967065-24967066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs538497780	chr3:24967088-24967089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs564076072	chr3:24967134-24967135	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs72068159	chr3:24967135-24967136	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs73049501	chr3:24967146-24967147	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs59384760	chr3:24967147-24967148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs565700887	chr3:24967163-24967164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs535282605	chr3:24967239-24967240	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs558423471	chr3:24967245-24967246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs138421466	chr3:24967279-24967280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs376063099	chr3:24967300-24967301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs369407008	chr3:24967328-24967329	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs554693982	chr3:24967336-24967337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs540672329	chr3:24967346-24967347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs537164085	chr3:24967403-24967404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs148852073	chr3:24967405-24967406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs143524091	chr3:24967430-24967431	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs560778681	chr3:24967442-24967443	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs546468265	chr3:24967454-24967455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs577483050	chr3:24967463-24967464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs137901475	chr3:24967464-24967465	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs573617228	chr3:24967471-24967472	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs541008357	chr3:24967488-24967489	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs560674808	chr3:24967495-24967496	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs575025134	chr3:24967537-24967538	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs143456565	chr3:24967553-24967554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs537239010	chr3:24967560-24967561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs546445732	chr3:24967568-24967569	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs564956443	chr3:24967601-24967602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs116377925	chr3:24967602-24967603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs74891453	chr3:24967618-24967619	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs181707690	chr3:24967640-24967641	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs202099678	chr3:24967648-24967649	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs548527523	chr3:24967668-24967669	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs146105841	chr3:24967673-24967674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:73)

Disease	PMID	Source
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	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
Oral squamous cell carcinoma	17134496	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Myelofibrosis	22110671	CNVD
Multiple myeloma	17550852	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24966600-24969000	Weak transcription	Fetal Lung	lung
2	chr3:24969000-24969400	Enhancers	Fetal Lung	lung
3	chr3:24969400-24975000	Weak transcription	Fetal Lung	lung
4	chr3:24970600-24971200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:24973600-24974400	Enhancers	Fetal Heart	heart
6	chr3:24975000-24976000	Enhancers	Fetal Kidney	kidney
7	chr3:24975000-24976000	Enhancers	Fetal Lung	lung
8	chr3:24976000-24976400	Weak transcription	Fetal Kidney	kidney
9	chr3:24976000-24976400	Weak transcription	Fetal Lung	lung
10	chr3:24976400-24976600	Enhancers	Fetal Kidney	kidney
11	chr3:24976400-24977600	Enhancers	Fetal Lung	lung
12	chr3:24976600-24976800	Enhancers	Fetal Heart	heart
13	chr3:24976600-24978800	Weak transcription	Fetal Kidney	kidney
14	chr3:24977600-24978000	Weak transcription	Fetal Lung	lung
15	chr3:24978000-24978800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:24978000-24979800	Enhancers	Fetal Lung	lung
17	chr3:24978600-24979200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:24978800-24979000	Enhancers	Fetal Kidney	kidney
19	chr3:24978800-24979200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:24978800-24979200	Enhancers	Right Atrium	heart
21	chr3:24978800-24979400	Enhancers	Placenta	Placenta
22	chr3:24979000-24979400	Enhancers	Fetal Muscle Trunk	muscle
23	chr3:24979200-24998400	Weak transcription	Right Atrium	heart
24	chr3:24979800-24980800	Weak transcription	Fetal Lung	lung
25	chr3:24980800-24981000	Enhancers	Fetal Lung	lung
26	chr3:24981000-24982200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:24985600-24986400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:24986000-24986200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:24986200-24986800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:24986800-24987000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:24986800-24987400	Enhancers	Fetal Muscle Leg	muscle
32	chr3:24987000-24996800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:24988800-24989400	Enhancers	Fetal Heart	heart
34	chr3:24990200-24990600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:24991200-24991400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:24991400-24991600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
37	chr3:24992600-24993000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr3:24992800-24993000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:24992800-24993400	Enhancers	Brain Substantia Nigra	brain
40	chr3:24993400-24994200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:24993600-24995000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
42	chr3:24993800-24994400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr3:24994000-24994200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
44	chr3:24994000-24994400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
45	chr3:24994000-24994400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
46	chr3:24994000-24994800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:24994000-24994800	Enhancers	Brain Germinal Matrix	brain
48	chr3:24994200-24994400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
49	chr3:24994200-24994800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:24994200-24994800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell

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