Variant report

Variant	nsv898758
Chromosome Location	chr12:10309477-10318497
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	BHLHE40	chr12:10313550-10313740	GM12878	blood:	n/a	n/a
2	CEBPB	chr12:10318141-10318362	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr12:10311120-10311270	GM12872	blood:	n/a	n/a
4	CTCF	chr12:10311300-10311450	GM12864	blood:	n/a	n/a
5	CTCF	chr12:10311200-10311350	GM12866	blood:	n/a	n/a
6	CTCF	chr12:10311120-10311270	GM12871	blood:	n/a	n/a
7	CTCF	chr12:10311140-10311290	HRPEpiC	eye:	n/a	n/a
8	CTCF	chr12:10316580-10316730	AG04450	lung:	n/a	n/a
9	CTCF	chr12:10315166-10315229	GM20000	blood:	n/a	n/a
10	CTCF	chr12:10311080-10311230	GM12865	blood:	n/a	n/a
11	CTCF	chr12:10311160-10311310	GM12873	blood:	n/a	n/a
12	FAM48A	chr12:10310820-10311004	GM12878	blood:	n/a	n/a
13	FOS	chr12:10313342-10313528	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr12:10313368-10313620	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr12:10310318-10310349	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr12:10311052-10311284	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr12:10310280-10310342	MCF10A-Er-Src	breast:	n/a	n/a
18	MAFK	chr12:10309520-10309675	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr12:10311858-10312120	NB4	blood:	n/a	n/a
20	MEF2A	chr12:10311266-10311650	GM12878	blood:	n/a	n/a
21	MEF2A	chr12:10313676-10314075	GM12878	blood:	n/a	chr12:10314009-10314023 chr12:10314009-10314024 chr12:10314012-10314021 chr12:10314007-10314028 chr12:10314008-10314024 chr12:10314011-10314022 chr12:10314007-10314028 chr12:10314010-10314021 chr12:10314010-10314025
22	MEF2C	chr12:10311240-10311751	GM12878	blood:	n/a	chr12:10311494-10311509
23	NFYB	chr12:10316616-10316789	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:10315193-10315246	MCF-7	breast:	n/a	n/a
25	POLR2A	chr12:10318158-10318780	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:10314775-10314909	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr12:10312587-10314323	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:10310454-10312373	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr12:10308740-10310038	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr12:10316525-10317463	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr12:10315672-10316283	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:10314654-10315323	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr12:10318152-10318347	Hela-S3	cervix:	n/a	n/a
34	SPI1	chr12:10313751-10313983	GM12891	blood:	n/a	chr12:10313885-10313894
35	SPI1	chr12:10315783-10316019	GM12878	blood:	n/a	n/a
36	SPI1	chr12:10315785-10316059	GM12891	blood:	n/a	n/a
37	SPI1	chr12:10315669-10316192	GM12878	blood:	n/a	n/a
38	SPI1	chr12:10313751-10313975	GM12878	blood:	n/a	chr12:10313885-10313894
39	SPI1	chr12:10315823-10315975	K562	blood:	n/a	n/a
40	SPI1	chr12:10315737-10316096	HL-60	blood:	n/a	n/a
41	SPI1	chr12:10313662-10314235	GM12878	blood:	n/a	chr12:10313885-10313894
42	SPI1	chr12:10315754-10316000	GM12891	blood:	n/a	n/a
43	SPI1	chr12:10315631-10316163	HL-60	blood:	n/a	n/a
44	SPI1	chr12:10315800-10315993	GM12878	blood:	n/a	n/a
45	ZNF263	chr12:10310824-10311398	HEK293-T-REx	kidney:	n/a	n/a
46	ZNF384	chr12:10311385-10311627	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10305112..10307480-chr12:10310212..10312398,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC7A-2	chr12:10312946-10313160	NONHSAT026866
2	lnc-CLEC7A-2	chr12:10312267-10312620	NONHSAT026866

No.	miRNA target gene	miRNA name	Chromosome Location
1	OLR1	hsa-miR-21-5p	chr12:10312424-10312418
2	OLR1	hsa-miR-98-5p	chr12:10312167-10312161
3	OLR1	hsa-miR-21-5p	chr12:10312419-10312440

Variant related genes	Relation type
TMEM52B	TF binding region
OLR1	TF binding region

Extended variants
information (count: 374 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:374 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12231585	chr12:10309477-10309478	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs576613620	chr12:10309489-10309490	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs533197058	chr12:10309506-10309507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs545726059	chr12:10309525-10309526	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs150095826	chr12:10309581-10309582	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs537870410	chr12:10309587-10309588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs541518517	chr12:10309608-10309609	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs561006233	chr12:10309635-10309636	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs34083880	chr12:10309654-10309655	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs543202733	chr12:10309703-10309704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs563506040	chr12:10309707-10309708	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs34501233	chr12:10309748-10309749	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs34956022	chr12:10309757-10309758	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs34300167	chr12:10309791-10309792	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs34352103	chr12:10309862-10309863	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs35366643	chr12:10309891-10309892	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs35297885	chr12:10309892-10309893	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs2171602	chr12:10309936-10309937	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs35386884	chr12:10309972-10309973	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs34331959	chr12:10309985-10309986	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs7298513	chr12:10309986-10309987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs550067135	chr12:10309988-10309989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs373055307	chr12:10310030-10310031	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs570248231	chr12:10310066-10310067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs371695252	chr12:10310067-10310068	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs539312980	chr12:10310119-10310120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs2130009	chr12:10310125-10310126	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs572458046	chr12:10310127-10310128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs3052162	chr12:10310130-10310131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs34012209	chr12:10310135-10310136	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs78080243	chr12:10310142-10310143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs397836970	chr12:10310144-10310145	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs76496525	chr12:10310145-10310146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs554948208	chr12:10310167-10310168	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs183884263	chr12:10310203-10310204	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs3994135	chr12:10310267-10310268	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs189149575	chr12:10310333-10310334	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs576654579	chr12:10310353-10310354	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs368343047	chr12:10310360-10310361	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs34908088	chr12:10310368-10310369	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs528073456	chr12:10310385-10310386	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs547829039	chr12:10310460-10310461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs11053645	chr12:10310471-10310472	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs530490268	chr12:10310488-10310489	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs550674660	chr12:10310533-10310534	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs570243149	chr12:10310534-10310535	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs182435737	chr12:10310538-10310539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs539273155	chr12:10310562-10310563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs185384876	chr12:10310587-10310588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs7964641	chr12:10310663-10310664	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:85)

Disease	PMID	Source
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Hepatocellular carcinoma	16750200	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21611746	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Squamous cell cancer	19607727	CNVD
Prostate cancer	16573809	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Acute myeloid leukemia	17268525	CNVD
Acute monocytic leukemia	16498392	CNVD
Prostate cancer	16461572	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Autism	22543975	CNVD

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10306400-10313400	Weak transcription	Hela-S3	cervix
2	chr12:10307000-10311400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:10307000-10312400	Weak transcription	Placenta	Placenta
4	chr12:10307000-10312800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:10307000-10313400	Weak transcription	Brain Anterior Caudate	brain
6	chr12:10307000-10318600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:10307000-10319800	Weak transcription	Right Atrium	heart
8	chr12:10307200-10311000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:10307200-10311200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:10307200-10311400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:10307400-10311400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:10309000-10311400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:10309000-10311600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:10310600-10311400	Weak transcription	GM12878-XiMat	blood
15	chr12:10311000-10312200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:10311200-10312400	Enhancers	Primary hematopoietic stem cells	blood
17	chr12:10311200-10315000	Enhancers	Primary B cells from cord blood	blood
18	chr12:10311400-10312200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:10311400-10312200	Enhancers	GM12878-XiMat	blood
20	chr12:10311400-10313200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr12:10311400-10313600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:10311400-10313600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr12:10311600-10316200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:10312200-10312600	Weak transcription	GM12878-XiMat	blood
25	chr12:10312400-10313200	Strong transcription	Placenta	Placenta
26	chr12:10312400-10313400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:10312600-10313400	Enhancers	GM12878-XiMat	blood
28	chr12:10312800-10313600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:10312800-10313600	Enhancers	Colon Smooth Muscle	Colon
30	chr12:10312800-10313600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr12:10312800-10313800	Enhancers	Fetal Stomach	stomach
32	chr12:10312800-10314400	Enhancers	Primary B cells from peripheral blood	blood
33	chr12:10313000-10313400	Enhancers	Fetal Heart	heart
34	chr12:10313200-10313600	Enhancers	Rectal Smooth Muscle	rectum
35	chr12:10313200-10313800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr12:10313200-10313800	Enhancers	NHEK	skin
37	chr12:10313200-10317600	Weak transcription	Placenta	Placenta
38	chr12:10313400-10313600	Enhancers	Primary hematopoietic stem cells	blood
39	chr12:10313400-10313600	Enhancers	Brain Anterior Caudate	brain
40	chr12:10313400-10313600	Flanking Active TSS	Fetal Heart	heart
41	chr12:10313400-10313600	Enhancers	Hela-S3	cervix
42	chr12:10313400-10313800	Flanking Active TSS	GM12878-XiMat	blood
43	chr12:10313600-10315800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr12:10313600-10318000	Weak transcription	Hela-S3	cervix
45	chr12:10313800-10314400	Enhancers	GM12878-XiMat	blood
46	chr12:10313800-10316200	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:10313800-10321800	Weak transcription	NHEK	skin
48	chr12:10314400-10316000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:10315000-10319600	Weak transcription	Primary B cells from cord blood	blood
50	chr12:10315800-10316200	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links