Variant report

Variant	nsv999459
Chromosome Location	chr3:272256-329970
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	ARID3A	chr3:291259-291870	HepG2	liver:	n/a	n/a
2	ARID3A	chr3:305517-307368	HepG2	liver:	n/a	n/a
3	ATF2	chr3:319829-320847	GM12878	blood:	n/a	n/a
4	ATF2	chr3:319964-320748	GM12878	blood:	n/a	n/a
5	ATF3	chr3:306304-306760	A549	lung:	n/a	n/a
6	BATF	chr3:319974-320310	GM12878	blood:	n/a	n/a
7	BATF	chr3:320384-320805	GM12878	blood:	n/a	n/a
8	BATF	chr3:319906-320293	GM12878	blood:	n/a	n/a
9	BCL11A	chr3:319927-320341	GM12878	blood:	n/a	chr3:320201-320210 chr3:320061-320069
10	BCL11A	chr3:319942-320280	GM12878	blood:	n/a	chr3:320201-320210 chr3:320061-320069
11	BCL3	chr3:306315-306750	A549	lung:	n/a	n/a
12	BCL3	chr3:320464-320727	GM12878	blood:	n/a	n/a
13	BCL3	chr3:306168-306863	A549	lung:	n/a	chr3:306285-306294 chr3:306282-306291
14	BCLAF1	chr3:320388-320763	GM12878	blood:	n/a	n/a
15	BHLHE40	chr3:306286-306823	HepG2	liver:	n/a	n/a
16	BHLHE40	chr3:319378-320826	GM12878	blood:	n/a	n/a
17	BRCA1	chr3:306406-306600	HepG2	liver:	n/a	n/a
18	BRCA1	chr3:306367-306903	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr3:291612-291803	H1-hESC	embryonic stem cell:	n/a	chr3:291705-291716
20	CEBPB	chr3:279116-279413	HepG2	liver:	n/a	chr3:279226-279239 chr3:279227-279238
21	CEBPB	chr3:279120-279410	A549	lung:	n/a	chr3:279226-279239 chr3:279227-279238
22	CEBPB	chr3:306264-306781	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
23	CEBPB	chr3:306278-306814	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
24	CEBPB	chr3:291583-291816	HepG2	liver:	n/a	chr3:291705-291716
25	CEBPB	chr3:306331-306724	HepG2	liver:	n/a	chr3:306463-306480
26	CEBPB	chr3:306097-307016	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
27	CEBPB	chr3:306264-306872	IMR90	lung:	n/a	chr3:306309-306322 chr3:306463-306480
28	CEBPB	chr3:291542-291836	HepG2	liver:	n/a	chr3:291705-291716
29	CEBPB	chr3:306177-307012	Hela-S3	cervix:	n/a	chr3:306309-306322 chr3:306463-306480
30	CEBPB	chr3:302689-302981	Hela-S3	cervix:	n/a	chr3:302812-302825
31	CEBPB	chr3:320077-320362	HepG2	liver:	n/a	chr3:320218-320229
32	CEBPB	chr3:306243-306864	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
33	CEBPB	chr3:306266-306559	MCF-7	breast:	n/a	chr3:306309-306322 chr3:306463-306480
34	CEBPB	chr3:306282-306969	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
35	CEBPB	chr3:306302-306622	MCF-7	breast:	n/a	chr3:306309-306322 chr3:306463-306480
36	CEBPB	chr3:306302-306792	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
37	CEBPB	chr3:284758-286178	IMR90	lung:	n/a	chr3:284916-284933 chr3:285984-286001 chr3:284887-284900
38	CEBPD	chr3:306328-306607	HepG2	liver:	n/a	n/a
39	CHD2	chr3:319756-320739	GM12878	blood:	n/a	n/a
40	CREB1	chr3:299561-299956	H1-hESC	embryonic stem cell:	n/a	n/a
41	CREB1	chr3:306269-306913	HepG2	liver:	n/a	n/a
42	CREB1	chr3:306373-306822	A549	lung:	n/a	n/a
43	CREB1	chr3:306196-306931	HepG2	liver:	n/a	n/a
44	CTCF	chr3:278947-279007	MCF-7	breast:	n/a	n/a
45	CTCF	chr3:287440-287590	GM12869	blood:	n/a	n/a
46	CTCF	chr3:278940-279009	GM19238	blood:	n/a	n/a
47	CTCF	chr3:287360-287510	MCF-7	breast:	n/a	n/a
48	CUX1	chr3:319594-320940	GM12878	blood:	n/a	n/a
49	E2F4	chr3:298337-298540	MCF10A-Er-Src	breast:	n/a	chr3:298525-298534
50	E2F4	chr3:306302-306616	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:285234-285284	HL-60	blood:	n/a
2	chr3:285234-285284	HEEpiC	esophagus:	n/a
3	chr3:285234-285284	ovcar-3	ovarian:	n/a
4	chr3:285234-285284	Hela-S3	cervix:	n/a
5	chr3:285234-285284	SK-N-MC	brain:	n/a
6	chr3:285234-285284	AoSMC	blood vessel:	n/a
7	chr3:285234-285284	PrEC	prostate:	n/a
8	chr3:285234-285284	NHDF-neo	bronchial:	n/a
9	chr3:285234-285284	GM12891	blood:	n/a
10	chr3:285234-285284	AG09319	gingival:	n/a
11	chr3:285234-285284	NH-A	brain:	n/a
12	chr3:285234-285284	HepG2	liver:	n/a
13	chr3:285234-285284	AG10803	skin:	n/a
14	chr3:285234-285284	U87	brain:	n/a
15	chr3:285234-285284	GM06990	blood:	n/a
16	chr3:285234-285284	ECC-1	luminal epithelium:	n/a
17	chr3:285234-285284	NHBE	bronchial:	n/a
18	chr3:285234-285284	HCPEpiC	choroid plexus:	n/a
19	chr3:285234-285284	HRE	kidney:	n/a
20	chr3:285234-285284	HNPCEpiC	eye:	n/a
21	chr3:285234-285284	AG04449	skin:	fetal
22	chr3:285234-285284	SAEC	small airway:	n/a
23	chr3:285234-285284	HMEC	breast:	n/a
24	chr3:285234-285284	A549	lung:	n/a
25	chr3:285234-285284	GM12892	blood:	n/a
26	chr3:285234-285284	MCF-7	breast:	n/a
27	chr3:285234-285284	MCF10A-Er-Src	breast:	n/a
28	chr3:285234-285284	HEK293	kidney:	embryo
29	chr3:285234-285284	HRCEpiC	kidney:	n/a
30	chr3:285234-285284	H1-hESC	embryonic stem cell:	embryo
31	chr3:285234-285284	HRPEpiC	eye:	n/a
32	chr3:285234-285284	HCM	heart:	n/a
33	chr3:285234-285284	ProgFib	skin:	n/a
34	chr3:285234-285284	AG04450	lung:	fetal
35	chr3:285234-285284	LNCaP	prostate:	n/a
36	chr3:285234-285284	IMR90	lung:	fetal
37	chr3:285234-285284	BE2_C	brain:	n/a
38	chr3:285234-285284	GM19239	blood:	n/a
39	chr3:285234-285284	RPTEC	kidney:	n/a
40	chr3:285234-285284	T-47D	breast:	n/a
41	chr3:285234-285284	HCF	heart:	n/a
42	chr3:285234-285284	SKMC	muscle:	n/a
43	chr3:285234-285284	SK-N-SH_RA	brain:	n/a
44	chr3:285234-285284	HUVEC	blood vessel:	n/a
45	chr3:285234-285284	Caco-2	colon:	n/a
46	chr3:285234-285284	BJ	skin:	n/a
47	chr3:285234-285284	Jurkat	blood:	n/a
48	chr3:285234-285284	K562	blood:	n/a
49	chr3:285234-285284	PFSK-1	brain:	n/a
50	chr3:285234-285284	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:297411..299702-chr3:300779..302869,2	K562	blood:
2	chr3:297411..299702-chr3:300779..302869,2	K562	blood:
3	chr3:291331..293955-chr3:294697..297452,2	MCF-7	breast:
4	chr3:291331..293955-chr3:294697..297452,2	MCF-7	breast:
5	chr3:321596..323780-chr3:337949..340526,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTN6-7	chr3:288251-288539	NONHSAT087560
2	lnc-CNTN6-7	chr3:288251-290282	NONHSAT087561
3	lnc-CNTN6-7	chr3:286296-286375	NONHSAT087560
4	lnc-CNTN6-7	chr3:286296-286375	NONHSAT087561

Variant related genes	Relation type
RNU6-1194P	TF binding region
RNU6-1194P	CpG island

Extended variants
information (count: 3151 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:3151 , 50 per page) page: 1 2 3 4 5 6 7 ... 64

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17264626	chr3:272256-272257	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs371820182	chr3:272302-272303	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs529819431	chr3:272321-272322	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs559781729	chr3:272334-272335	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs184675324	chr3:272387-272388	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs554193486	chr3:272390-272391	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs202236255	chr3:272433-272434	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs566107700	chr3:272448-272449	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs147843908	chr3:272483-272484	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs555109931	chr3:272556-272557	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs112060975	chr3:272563-272564	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs141491866	chr3:272567-272568	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs193276351	chr3:272572-272573	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs578131870	chr3:272609-272610	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs541345019	chr3:272610-272611	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs146981999	chr3:272617-272618	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs7625702	chr3:272641-272642	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs529654844	chr3:272658-272659	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs541486283	chr3:272659-272660	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs567430883	chr3:272664-272665	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs565641250	chr3:272666-272667	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs530679888	chr3:272852-272853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs531542603	chr3:272871-272872	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs138075020	chr3:272883-272884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs143634647	chr3:272920-272921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs184125531	chr3:272954-272955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs150107248	chr3:272955-272956	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs566038234	chr3:272989-272990	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs138477648	chr3:273004-273005	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs116493607	chr3:273005-273006	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs56760191	chr3:273031-273032	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs370117400	chr3:273059-273060	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs149241026	chr3:273076-273077	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs576985641	chr3:273112-273113	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs540889571	chr3:273129-273130	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs571493335	chr3:273225-273226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs538614836	chr3:273236-273237	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs5845954	chr3:273258-273259	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs572056629	chr3:273259-273260	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs72075331	chr3:273278-273279	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs552860948	chr3:273317-273318	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs553518688	chr3:273336-273337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs574051129	chr3:273359-273360	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs369311760	chr3:273406-273407	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs541422978	chr3:273416-273417	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs112447694	chr3:273449-273450	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs563338998	chr3:273472-273473	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs535909322	chr3:273477-273478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs332455	chr3:273503-273504	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs576184399	chr3:273508-273509	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

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	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	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
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:286 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:270200-272800	Enhancers	Brain Germinal Matrix	brain
2	chr3:270800-272600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:271000-274800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:271200-272400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:271400-272600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:271600-276000	Weak transcription	Brain Anterior Caudate	brain
7	chr3:271600-284800	Weak transcription	Ovary	ovary
8	chr3:271800-272600	Enhancers	Fetal Brain Female	brain
9	chr3:271800-277400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:272000-272800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:272000-274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:272200-274400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:272200-276000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:272200-276200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:272200-283800	Weak transcription	Fetal Brain Male	brain
16	chr3:272600-274400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:272600-274800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:272600-284400	Weak transcription	Fetal Brain Female	brain
19	chr3:273000-273200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:274400-275000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:274400-275000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:274600-275000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr3:274800-275000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr3:274800-275000	Enhancers	Right Atrium	heart
25	chr3:274800-275400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:275000-276200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:275000-276400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:275000-277000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:275200-277600	Weak transcription	Right Atrium	heart
30	chr3:276000-276600	Enhancers	Brain Angular Gyrus	brain
31	chr3:276000-276600	Enhancers	Brain Anterior Caudate	brain
32	chr3:276000-276600	Enhancers	Brain Hippocampus Middle	brain
33	chr3:276000-276600	Enhancers	Brain Substantia Nigra	brain
34	chr3:276200-276600	Enhancers	Primary B cells from peripheral blood	blood
35	chr3:276200-276600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:276200-276600	Enhancers	Brain Cingulate Gyrus	brain
37	chr3:276200-276600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr3:276200-277200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:276400-276600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr3:276600-284400	Weak transcription	Brain Anterior Caudate	brain
41	chr3:277400-277600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:277600-277800	Enhancers	Right Atrium	heart
43	chr3:277600-278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:278000-278200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:278200-283000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:280800-281000	Enhancers	Gastric	stomach
47	chr3:282800-283200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr3:283000-283200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:283000-283200	Enhancers	Brain Germinal Matrix	brain
50	chr3:283200-284400	Weak transcription	Fetal Lung	lung

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