Variant report

Variant	esv1819717
Chromosome Location	chr3:607873-660522
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	chr3:649451-649478	Hela-S3	cervix:	n/a	n/a
4	BRCA1	chr3:639591-639851	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr3:638934-639824	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr3:650024-650224	A549	lung:	n/a	chr3:650073-650084 chr3:650075-650084
7	CEBPB	chr3:649955-650248	IMR90	lung:	n/a	chr3:650073-650084 chr3:650075-650084
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	chr3:637765-638119	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr3:649124-649464	Hela-S3	cervix:	n/a	n/a
12	CHD2	chr3:639101-639345	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr3:658448-658477	ProgFib	skin:	n/a	n/a
14	CTCF	chr3:658486-658533	A549	lung:	n/a	n/a
15	CTCF	chr3:616998-617162	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr3:616980-617130	HEK293	kidney:	n/a	n/a
17	CTCF	chr3:623741-623815	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:616980-617130	HEEpiC	esophagus:	n/a	n/a
19	CTCF	chr3:655980-656130	GM12875	blood:	n/a	n/a
20	CTCF	chr3:612787-612876	GM13976	blood:	n/a	n/a
21	CTCF	chr3:616940-617090	A549	lung:	n/a	n/a
22	CTCF	chr3:617015-617090	LNCaP	prostate:	n/a	n/a
23	CTCF	chr3:641109-641158	ProgFib	skin:	n/a	n/a
24	CTCF	chr3:616960-617110	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr3:617062-617147	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:618424-618441	LNCaP	prostate:	n/a	n/a
27	CTCF	chr3:615631-615719	ProgFib	skin:	n/a	n/a
28	CTCF	chr3:659480-659630	GM12875	blood:	n/a	n/a
29	CTCF	chr3:616960-617110	SK-N-SH_RA	brain:	n/a	n/a
30	CTCF	chr3:616980-617130	Caco-2	colon:	n/a	n/a
31	CTCF	chr3:616960-617110	GM12865	blood:	n/a	n/a
32	CTCF	chr3:608164-608208	GM20000	blood:	n/a	n/a
33	CTCF	chr3:612832-612875	ProgFib	skin:	n/a	n/a
34	CTCF	chr3:616960-617110	GM12870	blood:	n/a	n/a
35	CTCF	chr3:616960-617110	WERI-Rb-1	eye:	n/a	n/a
36	CTCF	chr3:623765-623780	ProgFib	skin:	n/a	n/a
37	CTCF	chr3:650545-650626	ProgFib	skin:	n/a	n/a
38	CTCF	chr3:626000-626150	NHDF-neo	bronchial:	n/a	n/a
39	CTCF	chr3:616940-617090	HepG2	liver:	n/a	n/a
40	ELK1	chr3:639661-639775	Hela-S3	cervix:	n/a	n/a
41	ELK1	chr3:639134-639183	Hela-S3	cervix:	n/a	n/a
42	EP300	chr3:638941-639877	Hela-S3	cervix:	n/a	chr3:639272-639286
43	EP300	chr3:620995-621568	SK-N-SH	brain:	n/a	n/a
44	FOS	chr3:614457-614821	HUVEC	blood vessel:	n/a	n/a
45	FOXA2	chr3:623512-623895	A549	lung:	n/a	n/a
46	FOXP2	chr3:609428-609783	SK-N-MC	brain:	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	chr3:620053-620583	SH-SY5Y	brain:	n/a	chr3:620504-620525
50	GATA3	chr3:636965-637085	SH-SY5Y	brain:	n/a	n/a

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL5RA-14	chr3:659472-659997	NONHSAT087571
2	lnc-CHL1-6	chr3:608788-608866	ucscGeneNc_uc003boy_1
3	lnc-CHL1-3	chr3:633788-633866	NR_110118
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: 716 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:716 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543407068	chr3:607892-607893	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs2729248	chr3:607898-607899	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs201392226	chr3:607901-607902	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs547847543	chr3:607910-607911	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs183325845	chr3:607911-607912	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs12636550	chr3:608041-608042	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs187888687	chr3:608044-608045	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs529804132	chr3:608081-608082	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs548099690	chr3:608085-608086	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs191189150	chr3:608120-608121	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs537057926	chr3:608122-608123	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs111559494	chr3:608123-608124	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs538125856	chr3:608136-608137	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs148410451	chr3:608160-608161	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs564268535	chr3:608172-608173	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs142495769	chr3:608213-608214	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs116025227	chr3:608244-608245	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs184536881	chr3:608253-608254	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs533272408	chr3:608254-608255	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs147749742	chr3:608286-608287	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs576621826	chr3:608305-608306	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs2729249	chr3:608332-608333	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs146769144	chr3:608367-608368	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs71719082	chr3:608382-608383	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs2729250	chr3:608405-608406	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs541142805	chr3:608502-608503	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs559391991	chr3:608512-608513	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs547037637	chr3:608528-608529	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs9870187	chr3:608552-608553	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs541582177	chr3:608592-608593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs2729251	chr3:608623-608624	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs530756431	chr3:608641-608642	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs540814089	chr3:608666-608667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs74344583	chr3:608728-608729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs536787549	chr3:608752-608753	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs2729252	chr3:608767-608768	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs189806138	chr3:608853-608854	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs2729253	chr3:608929-608930	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs568117284	chr3:608986-608987	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs573524369	chr3:609038-609039	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs540567861	chr3:609089-609090	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs536848039	chr3:609109-609110	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs569275931	chr3:609110-609111	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs34743679	chr3:609136-609137	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs62236834	chr3:609152-609153	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs570228171	chr3:609175-609176	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs112097422	chr3:609245-609246	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs192729666	chr3:609255-609256	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs149258937	chr3:609260-609261	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs35134288	chr3:609263-609264	Enhancers Weak transcription	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:12 , 50 per page) page: 1

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

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