Variant report

Variant	esv1822857
Chromosome Location	chr3:604874-663411
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	chr3:639591-639851	Hela-S3	cervix:	n/a	n/a
3	BRCA1	chr3:649451-649478	Hela-S3	cervix:	n/a	n/a
4	BRCA1	chr3:638578-639330	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr3:637765-638119	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr3:649124-649464	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr3:650024-650224	A549	lung:	n/a	chr3:650073-650084 chr3:650075-650084
8	CEBPB	chr3:649955-650248	IMR90	lung:	n/a	chr3:650073-650084 chr3:650075-650084
9	CEBPB	chr3:638934-639824	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr3:650039-650244	HepG2	liver:	n/a	chr3:650073-650084 chr3:650075-650084
11	CEBPB	chr3:611097-611344	HepG2	liver:	n/a	chr3:611201-611212
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	chr3:616960-617110	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr3:617062-617147	MCF-7	breast:	n/a	n/a
16	CTCF	chr3:617015-617090	LNCaP	prostate:	n/a	n/a
17	CTCF	chr3:612832-612875	ProgFib	skin:	n/a	n/a
18	CTCF	chr3:616940-617090	HepG2	liver:	n/a	n/a
19	CTCF	chr3:658448-658477	ProgFib	skin:	n/a	n/a
20	CTCF	chr3:608164-608208	GM20000	blood:	n/a	n/a
21	CTCF	chr3:616940-617090	A549	lung:	n/a	n/a
22	CTCF	chr3:616980-617130	HEEpiC	esophagus:	n/a	n/a
23	CTCF	chr3:641109-641158	ProgFib	skin:	n/a	n/a
24	CTCF	chr3:662427-662492	GM20000	blood:	n/a	n/a
25	CTCF	chr3:659480-659630	GM12875	blood:	n/a	n/a
26	CTCF	chr3:616980-617130	HEK293	kidney:	n/a	n/a
27	CTCF	chr3:616960-617110	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr3:655980-656130	GM12875	blood:	n/a	n/a
29	CTCF	chr3:626000-626150	NHDF-neo	bronchial:	n/a	n/a
30	CTCF	chr3:616980-617130	Caco-2	colon:	n/a	n/a
31	CTCF	chr3:623741-623815	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:615631-615719	ProgFib	skin:	n/a	n/a
33	CTCF	chr3:623765-623780	ProgFib	skin:	n/a	n/a
34	CTCF	chr3:650545-650626	ProgFib	skin:	n/a	n/a
35	CTCF	chr3:658486-658533	A549	lung:	n/a	n/a
36	CTCF	chr3:616960-617110	WERI-Rb-1	eye:	n/a	n/a
37	CTCF	chr3:616998-617162	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr3:616960-617110	GM12865	blood:	n/a	n/a
39	CTCF	chr3:612787-612876	GM13976	blood:	n/a	n/a
40	CTCF	chr3:616960-617110	GM12870	blood:	n/a	n/a
41	CTCF	chr3:618424-618441	LNCaP	prostate:	n/a	n/a
42	ELK1	chr3:639661-639775	Hela-S3	cervix:	n/a	n/a
43	ELK1	chr3:639134-639183	Hela-S3	cervix:	n/a	n/a
44	EP300	chr3:638941-639877	Hela-S3	cervix:	n/a	chr3:639272-639286
45	EP300	chr3:620995-621568	SK-N-SH	brain:	n/a	n/a
46	FOS	chr3:614457-614821	HUVEC	blood vessel:	n/a	n/a
47	FOXA2	chr3:623512-623895	A549	lung:	n/a	n/a
48	FOXP2	chr3:609428-609783	SK-N-MC	brain:	n/a	n/a
49	GABPA	chr3:638980-639383	Hela-S3	cervix:	n/a	n/a
50	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

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	ENSG00000224957
2	lnc-CHL1-3	chr3:633788-633866	NR_110118
3	lnc-CHL1-6	chr3:608788-608866	ucscGeneNc_uc003boy_1
4	lnc-IL5RA-14	chr3:659472-659997	NONHSAT087571

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

Extended variants
information (count: 859 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:859 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs528678062	chr3:604895-604896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs562011462	chr3:604905-604906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs142560122	chr3:604911-604912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs185292242	chr3:604922-604923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs2729209	chr3:604939-604940	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs550842954	chr3:604990-604991	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs569193081	chr3:604997-604998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs189007367	chr3:605001-605002	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs35307795	chr3:605006-605007	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs192523427	chr3:605024-605025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs573248321	chr3:605066-605067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs146694541	chr3:605081-605082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs377483747	chr3:605090-605091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs555646935	chr3:605101-605102	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs573857433	chr3:605103-605104	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs77274071	chr3:605109-605110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs77818583	chr3:605154-605155	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs9846287	chr3:605162-605163	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs183460294	chr3:605168-605169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs560002982	chr3:605178-605179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs527424926	chr3:605212-605213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs551237074	chr3:605243-605244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs114381944	chr3:605268-605269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs139150045	chr3:605294-605295	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs529432161	chr3:605313-605314	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs2729219	chr3:605373-605374	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs115571225	chr3:605380-605381	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs539453737	chr3:605389-605390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs551793036	chr3:605403-605404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs116716761	chr3:605407-605408	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs534094806	chr3:605451-605452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs534314980	chr3:605484-605485	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs188232633	chr3:605510-605511	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs181069653	chr3:605524-605525	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs62236833	chr3:605527-605528	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs556184751	chr3:605537-605538	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs78041786	chr3:605570-605571	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs184820096	chr3:605623-605624	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs2729225	chr3:605628-605629	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs371518954	chr3:605639-605640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs35650816	chr3:605742-605743	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs571926225	chr3:605802-605803	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs577641044	chr3:605821-605822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs542349031	chr3:605842-605843	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs116770892	chr3:605847-605848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs529467569	chr3:605850-605851	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs35061349	chr3:605881-605882	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs76888417	chr3:605897-605898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs562931716	chr3:605929-605930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs80177877	chr3:606003-606004	Weak transcription 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:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:594600-607600	Weak transcription	Aorta	Aorta
2	chr3:603000-606000	Weak transcription	Fetal Brain Male	brain
3	chr3:606000-607000	Enhancers	Fetal Brain Male	brain
4	chr3:607000-610000	Weak transcription	Fetal Brain Male	brain
5	chr3:607600-608400	Enhancers	Aorta	Aorta
6	chr3:608800-610600	Enhancers	Brain Germinal Matrix	brain
7	chr3:610000-611200	Enhancers	Fetal Brain Male	brain
8	chr3:610200-610600	Enhancers	Ovary	ovary
9	chr3:611200-612400	Weak transcription	Fetal Brain Male	brain
10	chr3:612600-612800	Enhancers	Fetal Brain Male	brain
11	chr3:636400-642600	Enhancers	Hela-S3	cervix
12	chr3:639200-639800	Enhancers	Dnd41	blood
13	chr3:649000-650000	Enhancers	Hela-S3	cervix
14	chr3:649200-650200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:659600-660000	Active TSS	Spleen	Spleen

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