Variant report

Variant	nsv590996
Chromosome Location	chr3:94857157-94914290
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	chr3:94867079-94867278	GM12878	blood:	n/a	chr3:94867158-94867169
2	CEBPB	chr3:94873555-94874070	MCF-7	breast:	n/a	n/a
3	CEBPB	chr3:94908207-94908561	HepG2	liver:	n/a	chr3:94908377-94908386 chr3:94908375-94908386 chr3:94908375-94908388 chr3:94908377-94908388 chr3:94908487-94908499 chr3:94908377-94908386 chr3:94908375-94908388 chr3:94908377-94908386 chr3:94908372-94908389 chr3:94908377-94908386
4	CEBPB	chr3:94880952-94881302	A549	lung:	n/a	chr3:94881115-94881128 chr3:94881115-94881128 chr3:94881117-94881126 chr3:94881116-94881127 chr3:94881115-94881128 chr3:94881115-94881126
5	CEBPB	chr3:94873659-94874133	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr3:94880997-94881305	HepG2	liver:	n/a	chr3:94881115-94881128 chr3:94881115-94881128 chr3:94881117-94881126 chr3:94881116-94881127 chr3:94881115-94881128 chr3:94881115-94881126
7	CEBPB	chr3:94908204-94908562	IMR90	lung:	n/a	chr3:94908377-94908386 chr3:94908375-94908386 chr3:94908375-94908388 chr3:94908377-94908388 chr3:94908487-94908499 chr3:94908377-94908386 chr3:94908375-94908388 chr3:94908377-94908386 chr3:94908372-94908389 chr3:94908377-94908386
8	CEBPB	chr3:94908276-94908544	K562	blood:	n/a	chr3:94908377-94908386 chr3:94908375-94908386 chr3:94908375-94908388 chr3:94908377-94908388 chr3:94908487-94908499 chr3:94908377-94908386 chr3:94908375-94908388 chr3:94908377-94908386 chr3:94908372-94908389 chr3:94908377-94908386
9	CEBPB	chr3:94908217-94908539	A549	lung:	n/a	chr3:94908377-94908386 chr3:94908375-94908386 chr3:94908375-94908388 chr3:94908377-94908388 chr3:94908487-94908499 chr3:94908377-94908386 chr3:94908375-94908388 chr3:94908377-94908386 chr3:94908372-94908389 chr3:94908377-94908386
10	CEBPB	chr3:94859027-94859271	HepG2	liver:	n/a	n/a
11	CEBPB	chr3:94858964-94859274	IMR90	lung:	n/a	n/a
12	CEBPB	chr3:94865345-94865624	Hela-S3	cervix:	n/a	chr3:94865483-94865496
13	CEBPB	chr3:94873551-94874188	MCF-7	breast:	n/a	n/a
14	CTCF	chr3:94902959-94903153	MCF-7	breast:	n/a	n/a
15	CTCF	chr3:94891080-94891230	RPTEC	kidney:	n/a	n/a
16	CTCF	chr3:94870776-94870809	GM13976	blood:	n/a	n/a
17	CTCF	chr3:94902951-94903139	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:94902951-94903127	Gliobla	brain:	n/a	n/a
19	CTCF	chr3:94891065-94891193	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:94902966-94903154	MCF-7	breast:	n/a	n/a
21	CTCF	chr3:94902920-94903070	GM12872	blood:	n/a	n/a
22	CTCF	chr3:94890940-94891090	BE2_C	brain:	n/a	n/a
23	CTCF	chr3:94902980-94903130	WERI-Rb-1	eye:	n/a	n/a
24	CTCF	chr3:94903020-94903170	MCF-7	breast:	n/a	n/a
25	CTCF	chr3:94901753-94901799	GM20000	blood:	n/a	n/a
26	CTCF	chr3:94891000-94891150	MCF-7	breast:	n/a	n/a
27	CTCF	chr3:94902945-94903131	HepG2	liver:	n/a	n/a
28	CTCF	chr3:94903031-94903125	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr3:94902937-94903191	GM12878	blood:	n/a	n/a
30	CTCF	chr3:94900820-94900858	Spleen_OC	spleen:	n/a	n/a
31	CTCF	chr3:94902980-94903130	HepG2	liver:	n/a	n/a
32	CTCF	chr3:94902900-94903050	A549	lung:	n/a	n/a
33	CTCF	chr3:94901413-94901515	Kidney_OC	kidney:	n/a	n/a
34	CTCF	chr3:94891040-94891190	HBMEC	blood vessel:	n/a	n/a
35	CTCF	chr3:94902939-94903113	HepG2	liver:	n/a	n/a
36	CTCF	chr3:94902943-94903149	MCF-7	breast:	n/a	n/a
37	CTCF	chr3:94902920-94903070	WERI-Rb-1	eye:	n/a	n/a
38	CTCF	chr3:94902980-94903130	GM12875	blood:	n/a	n/a
39	CTCF	chr3:94902900-94903050	GM12872	blood:	n/a	n/a
40	CTCF	chr3:94902980-94903130	K562	blood:	n/a	n/a
41	CTCF	chr3:94903021-94903076	GM12891	blood:	n/a	n/a
42	CTCF	chr3:94902900-94903050	MCF-7	breast:	n/a	n/a
43	CTCF	chr3:94902900-94903050	GM12878	blood:	n/a	n/a
44	CTCF	chr3:94902957-94903127	K562	blood:	n/a	n/a
45	CTCF	chr3:94902980-94903130	HEK293	kidney:	n/a	n/a
46	CTCF	chr3:94891049-94891134	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr3:94902940-94903090	Caco-2	colon:	n/a	n/a
48	CTCF	chr3:94902969-94903136	MCF-7	breast:	n/a	n/a
49	CTCF	chr3:94902960-94903110	HepG2	liver:	n/a	n/a
50	CTCF	chr3:94902994-94903102	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:94912857..94914770-chr3:94921596..94924370,2	MCF-7	breast:
2	chr3:94852529..94855191-chr3:94858249..94861078,2	MCF-7	breast:
3	chr3:94881976..94883745-chr3:94887711..94889312,2	K562	blood:
4	chr3:94877501..94880060-chr3:94881740..94883902,2	MCF-7	breast:
5	chr3:94881976..94883745-chr3:94887711..94889312,2	K562	blood:
6	chr3:94877501..94880060-chr3:94881740..94883902,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NSUN3-1	chr3:94890764-94891221	NONHSAT090744
2	lnc-NSUN3-1	chr3:94857070-94857159	ENSG00000239589
3	lnc-NSUN3-1	chr3:94870874-94871353	ENSG00000239589
4	lnc-NSUN3-1	chr3:94857030-94857161	NONHSAT090743

Variant related genes	Relation type
RPS18P6	TF binding region

Extended variants
information (count: 564 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:564 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11925057	chr3:94857157-94857158	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs551349578	chr3:94857161-94857162	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs576879849	chr3:94863423-94863424	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs4407407	chr3:94863471-94863472	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs114270052	chr3:94863473-94863474	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs138811725	chr3:94863481-94863482	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs376780707	chr3:94863491-94863492	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs2310772	chr3:94863504-94863505	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs562053637	chr3:94863532-94863533	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs368700626	chr3:94863578-94863579	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs532215924	chr3:94863579-94863580	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs547450249	chr3:94863599-94863600	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs572357973	chr3:94863600-94863601	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs541091322	chr3:94863614-94863615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs564572655	chr3:94863701-94863702	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs568828382	chr3:94863720-94863721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs533301884	chr3:94863735-94863736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs552380681	chr3:94863796-94863797	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs192000308	chr3:94863813-94863814	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs551362197	chr3:94863835-94863836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs571412024	chr3:94863837-94863838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs9839723	chr3:94863866-94863867	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs536373233	chr3:94863878-94863879	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs35489947	chr3:94863909-94863910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs367574896	chr3:94863910-94863911	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs370438597	chr3:94863967-94863968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs1039646	chr3:94863994-94863995	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs115180857	chr3:94864019-94864020	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs144572177	chr3:94864068-94864069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs570505241	chr3:94864122-94864123	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs116597798	chr3:94864154-94864155	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs1021933	chr3:94864210-94864211	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs576191056	chr3:94864237-94864238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs73172320	chr3:94864273-94864274	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs72916635	chr3:94864275-94864276	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs572668185	chr3:94864297-94864298	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs534922927	chr3:94864314-94864315	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs148449484	chr3:94864342-94864343	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs576483084	chr3:94864383-94864384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs553876718	chr3:94864455-94864456	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs201422600	chr3:94864485-94864486	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs183016315	chr3:94864533-94864534	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs543895373	chr3:94864574-94864575	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs563772646	chr3:94864580-94864581	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs78521441	chr3:94864584-94864585	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs187681136	chr3:94864658-94864659	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs115343162	chr3:94864708-94864709	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs527618084	chr3:94864711-94864712	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs547365164	chr3:94864727-94864728	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs542779825	chr3:94864748-94864749	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
Cancer	20164920	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:94863400-94863600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:94863600-94864600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:94864400-94865200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:94864400-94865400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:94864600-94865200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:94864600-94865200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:94864600-94865200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr3:94864600-94865400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:94865000-94865200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:94865200-94870400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:94865200-94870400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:94865200-94870400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:94865400-94870400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:94870200-94870600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:94870200-94871000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:94870400-94870600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:94870400-94870800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:94870400-94870800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:94870400-94870800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:94870400-94870800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:94870400-94871000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:94870400-94871000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:94870800-94873600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:94873200-94874400	Enhancers	Hela-S3	cervix
25	chr3:94873400-94874400	Enhancers	NH-A	brain
26	chr3:94873600-94873800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:94873600-94873800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:94891000-94892000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:94891200-94891800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr3:94891400-94891800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:94891400-94891800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr3:94891400-94891800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:94891400-94891800	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:94891600-94891800	Enhancers	Liver	Liver
35	chr3:94902800-94903800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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