Variant report

Variant	esv1810402
Chromosome Location	chr3:610165-663266
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	BRCA1	chr3:638578-639330	Hela-S3	cervix:	n/a	n/a
3	BRCA1	chr3:639591-639851	Hela-S3	cervix:	n/a	n/a
4	BRCA1	chr3:649451-649478	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr3:649124-649464	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr3:638934-639824	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr3:637765-638119	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr3:650039-650244	HepG2	liver:	n/a	chr3:650073-650084 chr3:650075-650084
9	CEBPB	chr3:611097-611344	HepG2	liver:	n/a	chr3:611201-611212
10	CEBPB	chr3:649955-650248	IMR90	lung:	n/a	chr3:650073-650084 chr3:650075-650084
11	CEBPB	chr3:650024-650224	A549	lung:	n/a	chr3:650073-650084 chr3:650075-650084
12	CHD1	chr3:660628-660658	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD2	chr3:639101-639345	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr3:616940-617090	HepG2	liver:	n/a	n/a
15	CTCF	chr3:641109-641158	ProgFib	skin:	n/a	n/a
16	CTCF	chr3:650545-650626	ProgFib	skin:	n/a	n/a
17	CTCF	chr3:618424-618441	LNCaP	prostate:	n/a	n/a
18	CTCF	chr3:616940-617090	A549	lung:	n/a	n/a
19	CTCF	chr3:623765-623780	ProgFib	skin:	n/a	n/a
20	CTCF	chr3:617062-617147	MCF-7	breast:	n/a	n/a
21	CTCF	chr3:615631-615719	ProgFib	skin:	n/a	n/a
22	CTCF	chr3:616960-617110	SK-N-SH_RA	brain:	n/a	n/a
23	CTCF	chr3:616960-617110	WERI-Rb-1	eye:	n/a	n/a
24	CTCF	chr3:662427-662492	GM20000	blood:	n/a	n/a
25	CTCF	chr3:612832-612875	ProgFib	skin:	n/a	n/a
26	CTCF	chr3:617015-617090	LNCaP	prostate:	n/a	n/a
27	CTCF	chr3:616960-617110	GM12870	blood:	n/a	n/a
28	CTCF	chr3:658486-658533	A549	lung:	n/a	n/a
29	CTCF	chr3:616980-617130	HEK293	kidney:	n/a	n/a
30	CTCF	chr3:655980-656130	GM12875	blood:	n/a	n/a
31	CTCF	chr3:616980-617130	Caco-2	colon:	n/a	n/a
32	CTCF	chr3:623741-623815	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:626000-626150	NHDF-neo	bronchial:	n/a	n/a
34	CTCF	chr3:616960-617110	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr3:616980-617130	HEEpiC	esophagus:	n/a	n/a
36	CTCF	chr3:658448-658477	ProgFib	skin:	n/a	n/a
37	CTCF	chr3:659480-659630	GM12875	blood:	n/a	n/a
38	CTCF	chr3:612787-612876	GM13976	blood:	n/a	n/a
39	CTCF	chr3:616998-617162	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr3:616960-617110	GM12865	blood:	n/a	n/a
41	ELK1	chr3:639134-639183	Hela-S3	cervix:	n/a	n/a
42	ELK1	chr3:639661-639775	Hela-S3	cervix:	n/a	n/a
43	EP300	chr3:638941-639877	Hela-S3	cervix:	n/a	chr3:639272-639286
44	EP300	chr3:620995-621568	SK-N-SH	brain:	n/a	n/a
45	FOS	chr3:614457-614821	HUVEC	blood vessel:	n/a	n/a
46	FOXA2	chr3:623512-623895	A549	lung:	n/a	n/a
47	GABPA	chr3:638980-639383	Hela-S3	cervix:	n/a	n/a
48	GATA2	chr3:621236-621544	SH-SY5Y	brain:	n/a	chr3:621342-621349 chr3:621342-621353 chr3:621342-621349 chr3:621335-621356 chr3:621337-621353 chr3:621342-621349
49	GATA3	chr3:630942-631047	SH-SY5Y	brain:	n/a	n/a
50	GATA3	chr3:636965-637085	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:9533639..9536328-chr3:614645..617390,2	MCF-7	breast:
2	chr21:9517250..9519290-chr3:632442..635070,2	MCF-7	breast:
3	chr21:9537493..9539688-chr3:612236..614804,2	MCF-7	breast:

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

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

Extended variants
information (count: 638 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:638 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs189586850	chr3:610204-610205	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs180893987	chr3:610217-610218	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs77215919	chr3:610243-610244	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs77245502	chr3:610256-610257	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs569563204	chr3:610257-610258	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs561935069	chr3:610261-610262	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs141247287	chr3:610291-610292	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs544152789	chr3:610304-610305	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs185983137	chr3:610328-610329	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs28366716	chr3:610385-610386	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs2729259	chr3:610394-610395	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs528626215	chr3:610395-610396	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs191228103	chr3:610398-610399	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs150751222	chr3:610407-610408	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs535493700	chr3:610420-610421	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs550995580	chr3:610439-610440	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs576621630	chr3:610443-610444	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs569154931	chr3:610445-610446	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs76364066	chr3:610447-610448	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs558268648	chr3:610466-610467	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs537994043	chr3:610520-610521	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs556418149	chr3:610534-610535	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs375378603	chr3:610549-610550	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs566694627	chr3:610561-610562	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs2252871	chr3:610577-610578	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs555709663	chr3:610604-610605	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs183085692	chr3:610619-610620	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs544173593	chr3:610671-610672	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs556149013	chr3:610703-610704	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs73095120	chr3:610729-610730	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs74544540	chr3:610808-610809	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs199928546	chr3:610821-610822	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs559790689	chr3:610897-610898	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs185721955	chr3:610902-610903	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs190432398	chr3:610903-610904	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs77253459	chr3:610921-610922	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs529639341	chr3:610928-610929	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs550971175	chr3:610968-610969	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs569269839	chr3:611001-611002	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs533141164	chr3:611016-611017	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs182976269	chr3:611030-611031	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs9834879	chr3:611032-611033	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs534277690	chr3:611042-611043	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs374658221	chr3:611070-611071	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs187747018	chr3:611074-611075	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs79823039	chr3:611114-611115	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs538171889	chr3:611137-611138	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs556147901	chr3:611156-611157	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs193140572	chr3:611166-611167	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs544559479	chr3:611175-611176	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

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

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:608800-610600	Enhancers	Brain Germinal Matrix	brain
2	chr3:610000-611200	Enhancers	Fetal Brain Male	brain
3	chr3:610200-610600	Enhancers	Ovary	ovary
4	chr3:611200-612400	Weak transcription	Fetal Brain Male	brain
5	chr3:612600-612800	Enhancers	Fetal Brain Male	brain
6	chr3:636400-642600	Enhancers	Hela-S3	cervix
7	chr3:639200-639800	Enhancers	Dnd41	blood
8	chr3:649000-650000	Enhancers	Hela-S3	cervix
9	chr3:649200-650200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:659600-660000	Active TSS	Spleen	Spleen

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