Variant report

Variant	nsv1002942
Chromosome Location	chr3:261652-326537
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	chr3:319964-320748	GM12878	blood:	n/a	n/a
4	ATF2	chr3:319829-320847	GM12878	blood:	n/a	n/a
5	ATF3	chr3:306304-306760	A549	lung:	n/a	n/a
6	BACH1	chr3:271174-271333	K562	blood:	n/a	n/a
7	BATF	chr3:319906-320293	GM12878	blood:	n/a	n/a
8	BATF	chr3:319974-320310	GM12878	blood:	n/a	n/a
9	BATF	chr3:320384-320805	GM12878	blood:	n/a	n/a
10	BCL11A	chr3:319942-320280	GM12878	blood:	n/a	chr3:320201-320210 chr3:320061-320069
11	BCL11A	chr3:319927-320341	GM12878	blood:	n/a	chr3:320201-320210 chr3:320061-320069
12	BCL3	chr3:320464-320727	GM12878	blood:	n/a	n/a
13	BCL3	chr3:306315-306750	A549	lung:	n/a	n/a
14	BCL3	chr3:306168-306863	A549	lung:	n/a	chr3:306285-306294 chr3:306282-306291
15	BCLAF1	chr3:320388-320763	GM12878	blood:	n/a	n/a
16	BHLHE40	chr3:306286-306823	HepG2	liver:	n/a	n/a
17	BHLHE40	chr3:319378-320826	GM12878	blood:	n/a	n/a
18	BRCA1	chr3:306367-306903	Hela-S3	cervix:	n/a	n/a
19	BRCA1	chr3:306406-306600	HepG2	liver:	n/a	n/a
20	CEBPB	chr3:271018-271333	H1-hESC	embryonic stem cell:	n/a	chr3:271305-271317
21	CEBPB	chr3:291542-291836	HepG2	liver:	n/a	chr3:291705-291716
22	CEBPB	chr3:306264-306872	IMR90	lung:	n/a	chr3:306309-306322 chr3:306463-306480
23	CEBPB	chr3:279120-279410	A549	lung:	n/a	chr3:279226-279239 chr3:279227-279238
24	CEBPB	chr3:306302-306622	MCF-7	breast:	n/a	chr3:306309-306322 chr3:306463-306480
25	CEBPB	chr3:320077-320362	HepG2	liver:	n/a	chr3:320218-320229
26	CEBPB	chr3:284758-286178	IMR90	lung:	n/a	chr3:284916-284933 chr3:285984-286001 chr3:284887-284900
27	CEBPB	chr3:291612-291803	H1-hESC	embryonic stem cell:	n/a	chr3:291705-291716
28	CEBPB	chr3:306243-306864	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
29	CEBPB	chr3:306282-306969	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
30	CEBPB	chr3:306177-307012	Hela-S3	cervix:	n/a	chr3:306309-306322 chr3:306463-306480
31	CEBPB	chr3:306097-307016	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
32	CEBPB	chr3:302689-302981	Hela-S3	cervix:	n/a	chr3:302812-302825
33	CEBPB	chr3:306302-306792	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
34	CEBPB	chr3:306264-306781	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
35	CEBPB	chr3:306278-306814	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
36	CEBPB	chr3:279116-279413	HepG2	liver:	n/a	chr3:279226-279239 chr3:279227-279238
37	CEBPB	chr3:291583-291816	HepG2	liver:	n/a	chr3:291705-291716
38	CEBPB	chr3:306331-306724	HepG2	liver:	n/a	chr3:306463-306480
39	CEBPB	chr3:306266-306559	MCF-7	breast:	n/a	chr3:306309-306322 chr3:306463-306480
40	CEBPD	chr3:306328-306607	HepG2	liver:	n/a	n/a
41	CHD2	chr3:319756-320739	GM12878	blood:	n/a	n/a
42	CREB1	chr3:306373-306822	A549	lung:	n/a	n/a
43	CREB1	chr3:299561-299956	H1-hESC	embryonic stem cell:	n/a	n/a
44	CREB1	chr3:306196-306931	HepG2	liver:	n/a	n/a
45	CREB1	chr3:306269-306913	HepG2	liver:	n/a	n/a
46	CTCF	chr3:266691-266735	GM20000	blood:	n/a	n/a
47	CTCF	chr3:287440-287590	GM12869	blood:	n/a	n/a
48	CTCF	chr3:278947-279007	MCF-7	breast:	n/a	n/a
49	CTCF	chr3:278940-279009	GM19238	blood:	n/a	n/a
50	CTCF	chr3:287360-287510	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:271185-271235	LNCaP	prostate:	n/a
2	chr3:271185-271235	Hepatocyte	liver:	n/a
3	chr3:285234-285284	ECC-1	luminal epithelium:	n/a
4	chr3:285234-285284	ProgFib	skin:	n/a
5	chr3:271185-271235	GM12892	blood:	n/a
6	chr3:271185-271235	HNPCEpiC	eye:	n/a
7	chr3:271185-271235	AG10803	skin:	n/a
8	chr3:271185-271235	HUVEC	blood vessel:	n/a
9	chr3:271185-271235	Caco-2	colon:	n/a
10	chr3:285234-285284	ovcar-3	ovarian:	n/a
11	chr3:271185-271235	K562	blood:	n/a
12	chr3:285234-285284	HUVEC	blood vessel:	n/a
13	chr3:285234-285284	SKMC	muscle:	n/a
14	chr3:285234-285284	HepG2	liver:	n/a
15	chr3:271185-271235	NHBE	bronchial:	n/a
16	chr3:285234-285284	HAEpiC	amniotic membrane:	n/a
17	chr3:271185-271235	HL-60	blood:	n/a
18	chr3:285234-285284	HRCEpiC	kidney:	n/a
19	chr3:285234-285284	AG10803	skin:	n/a
20	chr3:285234-285284	AoSMC	blood vessel:	n/a
21	chr3:285234-285284	GM06990	blood:	n/a
22	chr3:271185-271235	HCF	heart:	n/a
23	chr3:285234-285284	AG09309	skin:	n/a
24	chr3:285234-285284	SK-N-SH	brain:	n/a
25	chr3:271185-271235	SK-N-SH_RA	brain:	n/a
26	chr3:285234-285284	NB4	blood:	n/a
27	chr3:285234-285284	LNCaP	prostate:	n/a
28	chr3:285234-285284	GM19239	blood:	n/a
29	chr3:271185-271235	GM12878	blood:	n/a
30	chr3:271185-271235	IMR90	lung:	fetal
31	chr3:271185-271235	T-47D	breast:	n/a
32	chr3:285234-285284	MCF-7	breast:	n/a
33	chr3:271185-271235	Hela-S3	cervix:	n/a
34	chr3:285234-285284	Caco-2	colon:	n/a
35	chr3:271185-271235	ECC-1	luminal epithelium:	n/a
36	chr3:285234-285284	HPAEpiC	pulmonary alveolar:	n/a
37	chr3:271185-271235	SAEC	small airway:	n/a
38	chr3:285234-285284	NHDF-neo	bronchial:	n/a
39	chr3:285234-285284	Hepatocyte	liver:	n/a
40	chr3:285234-285284	U87	brain:	n/a
41	chr3:271185-271235	SKMC	muscle:	n/a
42	chr3:285234-285284	HCT-116	colon:	n/a
43	chr3:285234-285284	HCF	heart:	n/a
44	chr3:285234-285284	HIPEpiC	eye:	n/a
45	chr3:285234-285284	SK-N-MC	brain:	n/a
46	chr3:285234-285284	HRE	kidney:	n/a
47	chr3:285234-285284	PANC-1	pancreas:	n/a
48	chr3:285234-285284	HNPCEpiC	eye:	n/a
49	chr3:271185-271235	PrEC	prostate:	n/a
50	chr3:271185-271235	SK-N-MC	brain:	n/a

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

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

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

Extended variants
information (count: 3461 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:3461 , 50 per page) page: 1 2 3 4 5 6 7 ... 70

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs461375	chr3:261652-261653	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs116084974	chr3:261657-261658	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs541198949	chr3:261671-261672	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs193124352	chr3:261728-261729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs535501951	chr3:261762-261763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs557387090	chr3:261772-261773	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs575653680	chr3:261773-261774	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs539591629	chr3:261775-261776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs77247915	chr3:261777-261778	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs143273520	chr3:261808-261809	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs559254706	chr3:261816-261817	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs572738075	chr3:261831-261832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs529914272	chr3:261839-261840	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs540117656	chr3:261851-261852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs368281987	chr3:261890-261891	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs555398626	chr3:261898-261899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs148328291	chr3:261901-261902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs636092	chr3:261902-261903	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs184272560	chr3:261943-261944	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs2088598	chr3:261978-261979	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs73090616	chr3:262026-262027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs530420161	chr3:262046-262047	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs188182828	chr3:262085-262086	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs528724342	chr3:262096-262097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs547243512	chr3:262104-262105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs551794549	chr3:262107-262108	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs141408084	chr3:262123-262124	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs180980006	chr3:262133-262134	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs570509464	chr3:262149-262150	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs112107270	chr3:262163-262164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs139972028	chr3:262171-262172	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs552491003	chr3:262182-262183	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs185451207	chr3:262207-262208	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs80199631	chr3:262208-262209	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs141898485	chr3:262216-262217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs568522309	chr3:262265-262266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs555593567	chr3:262266-262267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs573854002	chr3:262301-262302	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs544539738	chr3:262302-262303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs555873892	chr3:262314-262315	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs577747813	chr3:262319-262320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs545102140	chr3:262325-262326	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs560310746	chr3:262340-262341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs528660667	chr3:262359-262360	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs540474161	chr3:262363-262364	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs562354626	chr3:262386-262387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs188650443	chr3:262443-262444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs113228422	chr3:262458-262459	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs17007696	chr3:262461-262462	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs533179829	chr3:262505-262506	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:326 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:255400-265400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:265400-265800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:265800-267000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:266000-266200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:268200-268400	Enhancers	Ovary	ovary
6	chr3:268400-271000	Weak transcription	Ovary	ovary
7	chr3:269000-269200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr3:269200-270200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:269400-269600	Enhancers	Brain Anterior Caudate	brain
10	chr3:269400-271200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:269600-271000	Weak transcription	Brain Anterior Caudate	brain
12	chr3:270000-271800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:270200-270600	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr3:270200-272200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:270200-272800	Enhancers	Brain Germinal Matrix	brain
16	chr3:270400-271400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:270400-272000	Enhancers	HMEC	breast
18	chr3:270600-270800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:270600-271000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:270600-271000	Enhancers	NHEK	skin
21	chr3:270600-272000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:270800-271400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:270800-271800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:270800-272600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:271000-271200	Flanking Active TSS	Ovary	ovary
26	chr3:271000-271400	Enhancers	H9 Cell Line	embryonic stem cell
27	chr3:271000-271400	Flanking Active TSS	NHEK	skin
28	chr3:271000-271600	Enhancers	Brain Anterior Caudate	brain
29	chr3:271000-271800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr3:271000-271800	Enhancers	Fetal Lung	lung
31	chr3:271000-272000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:271000-272200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:271000-272200	Enhancers	Brain Hippocampus Middle	brain
34	chr3:271000-274800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:271200-271600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:271200-271600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr3:271200-271600	Active TSS	Ovary	ovary
38	chr3:271200-272000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:271200-272400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:271400-271800	Enhancers	NHEK	skin
41	chr3:271400-272200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:271400-272600	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr3:271600-272000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:271600-272200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:271600-272200	Enhancers	Fetal Brain Male	brain
46	chr3:271600-276000	Weak transcription	Brain Anterior Caudate	brain
47	chr3:271600-284800	Weak transcription	Ovary	ovary
48	chr3:271800-272200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr3:271800-272600	Enhancers	Fetal Brain Female	brain
50	chr3:271800-277400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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