Variant report

Variant	nsv1006735
Chromosome Location	chr3:256258-336454
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	chr3:331761-332103	GM12878	blood:	n/a	n/a
4	ATF2	chr3:319964-320748	GM12878	blood:	n/a	n/a
5	ATF2	chr3:319829-320847	GM12878	blood:	n/a	n/a
6	ATF3	chr3:306304-306760	A549	lung:	n/a	n/a
7	BACH1	chr3:271174-271333	K562	blood:	n/a	n/a
8	BATF	chr3:320384-320805	GM12878	blood:	n/a	n/a
9	BATF	chr3:259675-259847	GM12878	blood:	n/a	n/a
10	BATF	chr3:319906-320293	GM12878	blood:	n/a	n/a
11	BATF	chr3:319974-320310	GM12878	blood:	n/a	n/a
12	BCL11A	chr3:319942-320280	GM12878	blood:	n/a	chr3:320201-320210 chr3:320061-320069
13	BCL11A	chr3:319927-320341	GM12878	blood:	n/a	chr3:320201-320210 chr3:320061-320069
14	BCL3	chr3:306315-306750	A549	lung:	n/a	n/a
15	BCL3	chr3:320464-320727	GM12878	blood:	n/a	n/a
16	BCL3	chr3:306168-306863	A549	lung:	n/a	chr3:306285-306294 chr3:306282-306291
17	BCLAF1	chr3:320388-320763	GM12878	blood:	n/a	n/a
18	BHLHE40	chr3:260829-261058	GM12878	blood:	n/a	n/a
19	BHLHE40	chr3:306286-306823	HepG2	liver:	n/a	n/a
20	BHLHE40	chr3:260263-260618	GM12878	blood:	n/a	n/a
21	BHLHE40	chr3:319378-320826	GM12878	blood:	n/a	n/a
22	BRCA1	chr3:306406-306600	HepG2	liver:	n/a	n/a
23	BRCA1	chr3:306367-306903	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr3:306278-306814	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
25	CEBPB	chr3:302689-302981	Hela-S3	cervix:	n/a	chr3:302812-302825
26	CEBPB	chr3:306097-307016	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
27	CEBPB	chr3:306266-306559	MCF-7	breast:	n/a	chr3:306309-306322 chr3:306463-306480
28	CEBPB	chr3:306264-306872	IMR90	lung:	n/a	chr3:306309-306322 chr3:306463-306480
29	CEBPB	chr3:306177-307012	Hela-S3	cervix:	n/a	chr3:306309-306322 chr3:306463-306480
30	CEBPB	chr3:306264-306781	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
31	CEBPB	chr3:271018-271333	H1-hESC	embryonic stem cell:	n/a	chr3:271305-271317
32	CEBPB	chr3:279120-279410	A549	lung:	n/a	chr3:279226-279239 chr3:279227-279238
33	CEBPB	chr3:279116-279413	HepG2	liver:	n/a	chr3:279226-279239 chr3:279227-279238
34	CEBPB	chr3:320077-320362	HepG2	liver:	n/a	chr3:320218-320229
35	CEBPB	chr3:291583-291816	HepG2	liver:	n/a	chr3:291705-291716
36	CEBPB	chr3:284758-286178	IMR90	lung:	n/a	chr3:284916-284933 chr3:285984-286001 chr3:284887-284900
37	CEBPB	chr3:306243-306864	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
38	CEBPB	chr3:306331-306724	HepG2	liver:	n/a	chr3:306463-306480
39	CEBPB	chr3:306302-306622	MCF-7	breast:	n/a	chr3:306309-306322 chr3:306463-306480
40	CEBPB	chr3:306282-306969	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
41	CEBPB	chr3:291542-291836	HepG2	liver:	n/a	chr3:291705-291716
42	CEBPB	chr3:291612-291803	H1-hESC	embryonic stem cell:	n/a	chr3:291705-291716
43	CEBPB	chr3:306302-306792	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
44	CEBPD	chr3:306328-306607	HepG2	liver:	n/a	n/a
45	CHD2	chr3:319756-320739	GM12878	blood:	n/a	n/a
46	CREB1	chr3:299561-299956	H1-hESC	embryonic stem cell:	n/a	n/a
47	CREB1	chr3:306196-306931	HepG2	liver:	n/a	n/a
48	CREB1	chr3:306373-306822	A549	lung:	n/a	n/a
49	CREB1	chr3:306269-306913	HepG2	liver:	n/a	n/a
50	CTCF	chr3:278940-279009	GM19238	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:271185-271235	CMK	blood:	n/a
2	chr3:271185-271235	HRCEpiC	kidney:	n/a
3	chr3:285234-285284	IMR90	lung:	fetal
4	chr3:271185-271235	H1-hESC	embryonic stem cell:	embryo
5	chr3:285234-285284	SK-N-SH_RA	brain:	n/a
6	chr3:271185-271235	T-47D	breast:	n/a
7	chr3:285234-285284	HUVEC	blood vessel:	n/a
8	chr3:285234-285284	HRCEpiC	kidney:	n/a
9	chr3:271185-271235	HCF	heart:	n/a
10	chr3:271185-271235	SK-N-MC	brain:	n/a
11	chr3:285234-285284	SK-N-MC	brain:	n/a
12	chr3:271185-271235	NHDF-neo	bronchial:	n/a
13	chr3:285234-285284	MCF-7	breast:	n/a
14	chr3:271185-271235	AG10803	skin:	n/a
15	chr3:285234-285284	NHBE	bronchial:	n/a
16	chr3:285234-285284	H1-hESC	embryonic stem cell:	embryo
17	chr3:271185-271235	AG04450	lung:	fetal
18	chr3:271185-271235	BE2_C	brain:	n/a
19	chr3:285234-285284	HRPEpiC	eye:	n/a
20	chr3:271185-271235	LNCaP	prostate:	n/a
21	chr3:271185-271235	SAEC	small airway:	n/a
22	chr3:271185-271235	HCM	heart:	n/a
23	chr3:285234-285284	HEK293	kidney:	embryo
24	chr3:271185-271235	U87	brain:	n/a
25	chr3:285234-285284	NH-A	brain:	n/a
26	chr3:285234-285284	GM12891	blood:	n/a
27	chr3:285234-285284	Jurkat	blood:	n/a
28	chr3:285234-285284	HNPCEpiC	eye:	n/a
29	chr3:285234-285284	K562	blood:	n/a
30	chr3:285234-285284	SKMC	muscle:	n/a
31	chr3:271185-271235	GM12891	blood:	n/a
32	chr3:285234-285284	ovcar-3	ovarian:	n/a
33	chr3:285234-285284	HCPEpiC	choroid plexus:	n/a
34	chr3:285234-285284	NT2-D1	testis:	n/a
35	chr3:285234-285284	AG09309	skin:	n/a
36	chr3:285234-285284	AG09319	gingival:	n/a
37	chr3:271185-271235	HEK293	kidney:	embryo
38	chr3:271185-271235	Caco-2	colon:	n/a
39	chr3:285234-285284	HCF	heart:	n/a
40	chr3:285234-285284	PrEC	prostate:	n/a
41	chr3:271185-271235	HepG2	liver:	n/a
42	chr3:285234-285284	BJ	skin:	n/a
43	chr3:271185-271235	PFSK-1	brain:	n/a
44	chr3:271185-271235	SK-N-SH	brain:	n/a
45	chr3:285234-285284	GM12878	blood:	n/a
46	chr3:285234-285284	MCF10A-Er-Src	breast:	n/a
47	chr3:271185-271235	AoSMC	blood vessel:	n/a
48	chr3:285234-285284	LNCaP	prostate:	n/a
49	chr3:285234-285284	ProgFib	skin:	n/a
50	chr3:271185-271235	NHBE	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:297411..299702-chr3:300779..302869,2	K562	blood:
2	chr3:291331..293955-chr3:294697..297452,2	MCF-7	breast:
3	chr3:321596..323780-chr3:337949..340526,2	MCF-7	breast:
4	chr3:333238..334968-chr3:337821..339342,2	MCF-7	breast:
5	chr3:291331..293955-chr3:294697..297452,2	MCF-7	breast:
6	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	chr3:288251-288539	NONHSAT087560
4	lnc-CNTN6-7	chr3:286296-286375	NONHSAT087560

Variant related genes	Relation type
RNU6-1194P	TF binding region
CHL1	TF binding region
RNU6-1194P	CpG island
CHL1	CpG island

Extended variants
information (count: 4241 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:4241 , 50 per page) page: 1 2 3 4 5 6 7 ... 85

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2133402	chr3:256258-256259	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs140014726	chr3:256271-256272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs528307839	chr3:256277-256278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs553749600	chr3:256284-256285	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs540115657	chr3:256338-256339	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs561669675	chr3:256374-256375	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs528825780	chr3:256375-256376	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs371957456	chr3:256381-256382	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs368970287	chr3:256386-256387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs568812307	chr3:256427-256428	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs145337796	chr3:256433-256434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs571972790	chr3:256454-256455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs542690904	chr3:256456-256457	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571008416	chr3:256465-256466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs192705484	chr3:256467-256468	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs535258098	chr3:256525-256526	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs372733774	chr3:256529-256530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs386657251	chr3:256561-256562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs568784647	chr3:256562-256563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs535805166	chr3:256599-256600	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs116690282	chr3:256620-256621	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs113692906	chr3:256637-256638	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs5845952	chr3:256639-256640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs35265218	chr3:256640-256641	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs554486855	chr3:256656-256657	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs368771663	chr3:256665-256666	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs5845953	chr3:256666-256667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs184456736	chr3:256676-256677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs539910120	chr3:256713-256714	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs558000814	chr3:256744-256745	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs188198531	chr3:256757-256758	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs540053501	chr3:256802-256803	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs331867	chr3:256811-256812	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs201529127	chr3:256823-256824	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs544225738	chr3:256825-256826	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs562493584	chr3:256842-256843	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs140688468	chr3:256848-256849	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs532700319	chr3:256879-256880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs373591776	chr3:256905-256906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs532823562	chr3:256908-256909	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs112208174	chr3:256913-256914	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs551431963	chr3:256915-256916	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs547452984	chr3:256958-256959	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs191834384	chr3:257025-257026	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs528660613	chr3:257093-257094	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs67985544	chr3:257134-257135	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs568719889	chr3:257136-257137	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs77269964	chr3:257150-257151	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs184357747	chr3:257160-257161	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs569215723	chr3:257172-257173	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:85)

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
Hodgkin''s lymphoma	17606441	CNVD

Chromatin state (count:388 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:246200-258600	Weak transcription	Fetal Brain Female	brain
2	chr3:252800-256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:253200-258200	Weak transcription	Fetal Brain Male	brain
4	chr3:254400-258400	Weak transcription	Brain Germinal Matrix	brain
5	chr3:254600-258400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:255200-258400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:255400-265400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:257000-257200	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr3:257200-258200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:258200-258600	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr3:258200-259400	Enhancers	Fetal Brain Male	brain
12	chr3:258400-258600	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:258400-258800	Enhancers	Brain Hippocampus Middle	brain
14	chr3:258400-259400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:258400-261400	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:258600-258800	Enhancers	Brain Germinal Matrix	brain
17	chr3:258600-259400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:258600-259400	Enhancers	Fetal Brain Female	brain
19	chr3:258600-259400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:259200-259400	Enhancers	Esophagus	oesophagus
21	chr3:259200-260000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:259200-260000	Weak transcription	GM12878-XiMat	blood
23	chr3:259600-261400	Enhancers	Primary B cells from cord blood	blood
24	chr3:260000-261000	Enhancers	GM12878-XiMat	blood
25	chr3:265400-265800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:265800-267000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:266000-266200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:268200-268400	Enhancers	Ovary	ovary
29	chr3:268400-271000	Weak transcription	Ovary	ovary
30	chr3:269000-269200	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr3:269200-270200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:269400-269600	Enhancers	Brain Anterior Caudate	brain
33	chr3:269400-271200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:269600-271000	Weak transcription	Brain Anterior Caudate	brain
35	chr3:270000-271800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:270200-270600	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr3:270200-272200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:270200-272800	Enhancers	Brain Germinal Matrix	brain
39	chr3:270400-271400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:270400-272000	Enhancers	HMEC	breast
41	chr3:270600-270800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr3:270600-271000	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr3:270600-271000	Enhancers	NHEK	skin
44	chr3:270600-272000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:270800-271400	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr3:270800-271800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:270800-272600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:271000-271200	Flanking Active TSS	Ovary	ovary
49	chr3:271000-271400	Enhancers	H9 Cell Line	embryonic stem cell
50	chr3:271000-271400	Flanking Active TSS	NHEK	skin

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