Variant report

Variant	nsv965197
Chromosome Location	chr3:112238965-112250194
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	chr3:112250194-112250459	HepG2	liver:	n/a	n/a
2	BCL3	chr3:112245548-112245831	GM12878	blood:	n/a	n/a
3	CTCF	chr3:112250109-112250574	A549	lung:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
4	CTCF	chr3:112238900-112239050	SAEC	small airway:	n/a	n/a
5	CTCF	chr3:112239380-112239530	AG10803	skin:	n/a	n/a
6	CTCF	chr3:112250190-112250431	A549	lung:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
7	CTCF	chr3:112250055-112250580	HCT-116	colon:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
8	CTCF	chr3:112250151-112250591	GM12878	blood:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
9	CTCF	chr3:112250180-112250330	GM12864	blood:	n/a	n/a
10	CTCF	chr3:112239040-112239190	AG09319	gingival:	n/a	n/a
11	CTCF	chr3:112238820-112238970	HCM	heart:	n/a	n/a
12	CTCF	chr3:112250144-112250572	K562	blood:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
13	CTCF	chr3:112250180-112250330	HCT-116	colon:	n/a	n/a
14	CTCF	chr3:112243706-112243757	LNCaP	prostate:	n/a	n/a
15	CTCF	chr3:112250123-112250598	MCF-7	breast:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
16	CTCF	chr3:112250155-112250586	IMR90	lung:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
17	CTCF	chr3:112249600-112249750	NHDF-neo	bronchial:	n/a	n/a
18	CTCF	chr3:112250194-112250510	A549	lung:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
19	CTCF	chr3:112249437-112250669	A549	lung:	n/a	chr3:112250359-112250375 chr3:112250358-112250376 chr3:112250365-112250372 chr3:112250353-112250374
20	CTCF	chr3:112238960-112239110	BJ	skin:	n/a	n/a
21	CTCF	chr3:112239500-112239650	GM06990	blood:	n/a	n/a
22	CTCF	chr3:112237953-112239196	A549	lung:	n/a	chr3:112238428-112238446 chr3:112238423-112238444
23	EP300	chr3:112249266-112249884	A549	lung:	n/a	n/a
24	FOS	chr3:112249612-112249695	MCF10A-Er-Src	breast:	n/a	n/a
25	FOSL2	chr3:112249356-112249837	A549	lung:	n/a	n/a
26	FOSL2	chr3:112249364-112249781	A549	lung:	n/a	n/a
27	MAFF	chr3:112244103-112244174	HepG2	liver:	n/a	chr3:112244132-112244150
28	PBX3	chr3:112245369-112245579	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:112246198-112246205	MCF-7	breast:	n/a	n/a
30	POLR2A	chr3:112245902-112245928	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:112247982-112248061	ProgFib	skin:	n/a	n/a
32	POLR2A	chr3:112247843-112248321	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr3:112245721-112246006	ProgFib	skin:	n/a	n/a
34	POLR2A	chr3:112239442-112239560	MCF-7	breast:	n/a	n/a
35	POLR2A	chr3:112245870-112245894	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:112245771-112246198	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:112241380-112241413	MCF-7	breast:	n/a	n/a
38	POLR2A	chr3:112247074-112248291	K562	blood:	n/a	n/a
39	POLR2A	chr3:112245995-112246206	K562	blood:	n/a	n/a
40	POLR2A	chr3:112245738-112246064	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:112242401-112242479	K562	blood:	n/a	n/a
42	POLR2A	chr3:112245956-112246188	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr3:112239429-112239509	ProgFib	skin:	n/a	n/a
44	POLR2A	chr3:112245960-112246113	MCF-7	breast:	n/a	n/a
45	POLR2A	chr3:112245941-112246044	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:112248252-112248281	ProgFib	skin:	n/a	n/a
47	POLR2A	chr3:112242682-112242858	MCF10A-Er-Src	breast:	n/a	n/a
48	RAD21	chr3:112250190-112250594	A549	lung:	n/a	chr3:112250356-112250375 chr3:112250365-112250374
49	RAD21	chr3:112250176-112250534	Hela-S3	cervix:	n/a	chr3:112250356-112250375 chr3:112250365-112250374
50	RAD21	chr3:112250164-112250656	HCT-116	colon:	n/a	chr3:112250356-112250375 chr3:112250365-112250374

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112011976..112013367-chr3:112237943..112239384,10	MCF-7	breast:
2	chr3:112011899..112013194-chr3:112237762..112239193,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATG3-1	chr3:112244395-112246989	NONHSAT091182

Variant related genes	Relation type
OR7E100P	TF binding region
ENSG00000172139	chromatin interactions
CHUK	miRNA target sites

Extended variants
information (count: 483 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:483 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540460335	chr3:112239002-112239003	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs553884984	chr3:112239006-112239007	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs553629446	chr3:112239025-112239026	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs146287154	chr3:112239029-112239030	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs188952885	chr3:112239038-112239039	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs557799703	chr3:112239040-112239041	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs13070342	chr3:112239056-112239057	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs137878947	chr3:112239059-112239060	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs531224547	chr3:112239065-112239066	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs542196728	chr3:112239099-112239100	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs544477559	chr3:112239104-112239105	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs142389807	chr3:112239132-112239133	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs193084835	chr3:112239217-112239218	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs138876349	chr3:112239229-112239230	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs546831245	chr3:112239235-112239236	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs143883484	chr3:112239275-112239276	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs115980854	chr3:112239321-112239322	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs183252572	chr3:112239369-112239370	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs569197458	chr3:112239371-112239372	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs115858611	chr3:112239385-112239386	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs540196340	chr3:112239460-112239461	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs72938475	chr3:112239461-112239462	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs148628944	chr3:112239470-112239471	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs187366652	chr3:112239497-112239498	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs191562279	chr3:112239599-112239600	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs554054634	chr3:112239628-112239629	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs545813364	chr3:112239634-112239635	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs184039179	chr3:112239637-112239638	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs188091574	chr3:112239724-112239725	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs72938476	chr3:112239736-112239737	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs544641372	chr3:112239760-112239761	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs564431523	chr3:112239761-112239762	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs577965930	chr3:112239791-112239792	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs373525066	chr3:112239794-112239795	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs540528276	chr3:112239802-112239803	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs72938477	chr3:112239813-112239814	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs529478228	chr3:112239819-112239820	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs549427836	chr3:112239821-112239822	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs192430118	chr3:112239823-112239824	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs531721640	chr3:112239830-112239831	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs528596340	chr3:112239850-112239851	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs74344414	chr3:112239851-112239852	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs185678583	chr3:112239917-112239918	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs534031510	chr3:112240003-112240004	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs190549822	chr3:112240041-112240042	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs182434214	chr3:112240068-112240069	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs66486470	chr3:112240076-112240077	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs185913439	chr3:112240127-112240128	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs189165434	chr3:112240148-112240149	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs538244855	chr3:112240164-112240165	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	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
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
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Basal cell lymphoma	21115979	CNVD
Attention deficit hyperactivity disorder	22180640	CNVD

Chromatin state (count:366 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112218800-112241600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
3	chr3:112231600-112246800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:112234000-112247600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:112235600-112239800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:112235600-112243000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:112237000-112245400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:112237000-112247000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:112237200-112245600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:112237200-112247400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:112237200-112254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:112237400-112245400	Weak transcription	Primary B cells from cord blood	blood
14	chr3:112237600-112242600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:112237800-112245200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:112238000-112245800	Weak transcription	Primary T cells from cord blood	blood
17	chr3:112238200-112239400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:112238200-112245600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:112238200-112245800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:112238200-112247000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:112238200-112247400	Weak transcription	GM12878-XiMat	blood
22	chr3:112238600-112245800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:112238600-112249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:112238800-112240600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:112238800-112242400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:112238800-112245600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:112238800-112246000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:112239000-112239200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr3:112239000-112243200	Weak transcription	Fetal Stomach	stomach
30	chr3:112239200-112239800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:112239400-112239600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr3:112239400-112240600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:112239400-112242400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:112239800-112240400	Enhancers	Primary hematopoietic stem cells	blood
36	chr3:112239800-112240400	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr3:112239800-112245800	Weak transcription	Brain Germinal Matrix	brain
38	chr3:112239800-112247200	Weak transcription	Lung	lung
39	chr3:112239800-112247400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:112239800-112247800	Weak transcription	Aorta	Aorta
41	chr3:112239800-112247800	Weak transcription	Esophagus	oesophagus
42	chr3:112240000-112245800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:112240400-112243000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:112240400-112243000	Weak transcription	Left Ventricle	heart
45	chr3:112240400-112245800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:112240600-112243200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:112240600-112246600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:112240800-112242400	Weak transcription	Brain Anterior Caudate	brain
49	chr3:112240800-112242600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:112241000-112242800	Weak transcription	Adipose Nuclei	Adipose

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