Variant report

Variant	nsv972956
Chromosome Location	chr11:5838557-5842082
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	ATF1	chr11:5841202-5841334	K562	blood:	n/a	n/a
2	EBF1	chr11:5839416-5840361	GM12878	blood:	n/a	chr11:5839662-5839673 chr11:5839664-5839673 chr11:5839662-5839675 chr11:5839663-5839673 chr11:5839664-5839673
3	EBF1	chr11:5839448-5839917	GM12878	blood:	n/a	chr11:5839662-5839673 chr11:5839664-5839673 chr11:5839662-5839675 chr11:5839663-5839673 chr11:5839664-5839673
4	EBF1	chr11:5839411-5839898	GM12878	blood:	n/a	chr11:5839662-5839673 chr11:5839664-5839673 chr11:5839662-5839675 chr11:5839663-5839673 chr11:5839664-5839673
5	ELK1	chr11:5839868-5840125	GM12878	blood:	n/a	n/a
6	EP300	chr11:5839921-5839981	K562	blood:	n/a	n/a
7	IRF1	chr11:5839721-5839990	K562	blood:	n/a	chr11:5839903-5839917 chr11:5839901-5839911 chr11:5839895-5839909 chr11:5839895-5839912 chr11:5839899-5839919 chr11:5839897-5839911 chr11:5839901-5839915 chr11:5839899-5839910 chr11:5839907-5839917
8	IRF1	chr11:5839651-5840110	K562	blood:	n/a	chr11:5839903-5839917 chr11:5839901-5839911 chr11:5839895-5839909 chr11:5839895-5839912 chr11:5839899-5839919 chr11:5839897-5839911 chr11:5839901-5839915 chr11:5839899-5839910 chr11:5839907-5839917
9	IRF1	chr11:5839497-5840155	K562	blood:	n/a	chr11:5839903-5839917 chr11:5839901-5839911 chr11:5839895-5839909 chr11:5839895-5839912 chr11:5839899-5839919 chr11:5839897-5839911 chr11:5839901-5839915 chr11:5839899-5839910 chr11:5839907-5839917
10	MAZ	chr11:5839870-5839943	GM12878	blood:	n/a	n/a
11	MXI1	chr11:5839824-5840004	GM12878	blood:	n/a	n/a
12	MYC	chr11:5841673-5841773	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr11:5841900-5842027	A549	lung:	n/a	n/a
14	POLR2A	chr11:5838983-5839183	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr11:5840794-5840910	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr11:5841157-5841283	MCF10A-Er-Src	breast:	n/a	n/a
17	RCOR1	chr11:5839626-5839931	GM12878	blood:	n/a	n/a
18	RFX5	chr11:5840851-5840858	K562	blood:	n/a	n/a
19	STAT3	chr11:5839738-5839753	GM12878	blood:	n/a	n/a
20	STAT3	chr11:5839653-5839743	MCF10A-Er-Src	breast:	n/a	n/a
21	TBP	chr11:5839803-5839974	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:5841688-5841738	Hela-S3	cervix:	n/a
2	chr11:5841688-5841738	U87	brain:	n/a
3	chr11:5841688-5841738	NHBE	bronchial:	n/a
4	chr11:5841688-5841738	HMEC	breast:	n/a
5	chr11:5841482-5841532	HRPEpiC	eye:	n/a
6	chr11:5841482-5841532	HNPCEpiC	eye:	n/a
7	chr11:5841482-5841532	ECC-1	luminal epithelium:	n/a
8	chr11:5841482-5841532	SKMC	muscle:	n/a
9	chr11:5841482-5841532	SK-N-SH	brain:	n/a
10	chr11:5841688-5841738	HAEpiC	amniotic membrane:	n/a
11	chr11:5841688-5841738	GM12892	blood:	n/a
12	chr11:5841688-5841738	BE2_C	brain:	n/a
13	chr11:5841482-5841532	SAEC	small airway:	n/a
14	chr11:5841482-5841532	AG04449	skin:	fetal
15	chr11:5841482-5841532	Jurkat	blood:	n/a
16	chr11:5841482-5841532	HEK293	kidney:	embryo
17	chr11:5841482-5841532	NHDF-neo	bronchial:	n/a
18	chr11:5841482-5841532	Caco-2	colon:	n/a
19	chr11:5841482-5841532	MCF-7	breast:	n/a
20	chr11:5841688-5841738	GM06990	blood:	n/a
21	chr11:5841688-5841738	SAEC	small airway:	n/a
22	chr11:5841688-5841738	NB4	blood:	n/a
23	chr11:5841688-5841738	Hepatocyte	liver:	n/a
24	chr11:5841688-5841738	GM19239	blood:	n/a
25	chr11:5841688-5841738	LNCaP	prostate:	n/a
26	chr11:5841688-5841738	PFSK-1	brain:	n/a
27	chr11:5841688-5841738	HIPEpiC	eye:	n/a
28	chr11:5841482-5841532	Hela-S3	cervix:	n/a
29	chr11:5841482-5841532	NHBE	bronchial:	n/a
30	chr11:5841688-5841738	HPAEpiC	pulmonary alveolar:	n/a
31	chr11:5841482-5841532	NH-A	brain:	n/a
32	chr11:5841482-5841532	GM12891	blood:	n/a
33	chr11:5841688-5841738	PANC-1	pancreas:	n/a
34	chr11:5841688-5841738	HEK293	kidney:	embryo
35	chr11:5841482-5841532	SK-N-MC	brain:	n/a
36	chr11:5841688-5841738	NHDF-neo	bronchial:	n/a
37	chr11:5841688-5841738	PrEC	prostate:	n/a
38	chr11:5841482-5841532	GM06990	blood:	n/a
39	chr11:5841688-5841738	MCF10A-Er-Src	breast:	n/a
40	chr11:5841688-5841738	SK-N-SH_RA	brain:	n/a
41	chr11:5841482-5841532	U87	brain:	n/a
42	chr11:5841482-5841532	HIPEpiC	eye:	n/a
43	chr11:5841688-5841738	NH-A	brain:	n/a
44	chr11:5841688-5841738	SK-N-MC	brain:	n/a
45	chr11:5841688-5841738	AG10803	skin:	n/a
46	chr11:5841688-5841738	AG09309	skin:	n/a
47	chr11:5841482-5841532	HRCEpiC	kidney:	n/a
48	chr11:5841482-5841532	NB4	blood:	n/a
49	chr11:5841482-5841532	ovcar-3	ovarian:	n/a
50	chr11:5841688-5841738	HEEpiC	esophagus:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5831234..5833906-chr11:5837299..5840310,4	K562	blood:
2	chr11:5831234..5833906-chr11:5837299..5840310,3	K562	blood:

Variant related genes	Relation type
OR52N2	TF binding region
OR52N2	CpG island

Extended variants
information (count: 172 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:172 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547066184	chr11:5838561-5838562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs562069597	chr11:5838562-5838563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs552720773	chr11:5838592-5838593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs116297214	chr11:5838606-5838607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs370579548	chr11:5838662-5838663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs79466231	chr11:5838691-5838692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs111491475	chr11:5838713-5838714	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs193057545	chr11:5838804-5838805	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs544387106	chr11:5838826-5838827	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs73394353	chr11:5838873-5838874	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs116682695	chr11:5838884-5838885	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs533776513	chr11:5838885-5838886	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs10742798	chr11:5838913-5838914	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs576383082	chr11:5838939-5838940	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs567268631	chr11:5838981-5838982	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs76865460	chr11:5839035-5839036	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs12361759	chr11:5839036-5839037	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs143620131	chr11:5839040-5839041	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs575491068	chr11:5839146-5839147	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs184212416	chr11:5839151-5839152	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs145973005	chr11:5839182-5839183	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs148207769	chr11:5839183-5839184	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs540504485	chr11:5839209-5839210	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs141215066	chr11:5839222-5839223	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs73394356	chr11:5839224-5839225	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs528671730	chr11:5839260-5839261	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs73394358	chr11:5839283-5839284	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs150709564	chr11:5839285-5839286	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs188366471	chr11:5839286-5839287	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs551631968	chr11:5839297-5839298	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs10769249	chr11:5839326-5839327	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs527450023	chr11:5839373-5839374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs548930861	chr11:5839406-5839407	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs73394360	chr11:5839408-5839409	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs537560532	chr11:5839454-5839455	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs550123362	chr11:5839462-5839463	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs35574431	chr11:5839473-5839474	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs553036612	chr11:5839478-5839479	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs555878949	chr11:5839493-5839494	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs193021108	chr11:5839517-5839518	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs184574641	chr11:5839521-5839522	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs558413146	chr11:5839525-5839526	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs570134098	chr11:5839630-5839631	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs73394362	chr11:5839683-5839684	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs540792190	chr11:5839727-5839728	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs562822128	chr11:5839732-5839733	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs139017128	chr11:5839740-5839741	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs10838680	chr11:5839744-5839745	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs562998501	chr11:5839795-5839796	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs188551847	chr11:5839798-5839799	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
Neuroblastoma	18923191	CNVD
Breast cancer	19432969	CNVD
Alzheimer''s disease	17576883	CNVD
Long-qt syndrome	17576883	CNVD
Emphysema	19352772	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Chordoma	18071362	CNVD
Breast cancer	16608533	CNVD
Cancer	21183584	CNVD
Gastric adenocarcinoma	19115996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	19759907	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Thyroid cancer	19087340	CNVD
Melanoma	18172304	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Wilms tumour	21544195	CNVD
Parathyroid adenoma	22454399	CNVD
Chordoma	21602918	CNVD
Breast cancer	21949216	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	19222835	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Beckwith-Wiedemann syndrome	21518781	CNVD
Wilms tumour	21518781	CNVD
Hepatoblastoma	21518781	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Gastric cancer	17908304	CNVD
Barrett''s syndrome	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Multiple myeloma	20724749	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Myelofibrosis	22110671	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Neuroblastoma	21124317	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Schizophrenia	21399695	CNVD
Gastric cancer	16891809	CNVD
Cancer	17160897	CNVD
Multiple myeloma	16616336	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	23613489	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Ependymoma	20639864	CNVD
Type 2 diabetes	21526130	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5837200-5839400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr11:5837600-5839400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:5837600-5841200	Weak transcription	K562	blood
4	chr11:5837600-5844600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:5837800-5839400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:5838000-5839200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:5838000-5839400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr11:5838000-5839600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:5838000-5839600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:5839000-5839600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:5839200-5839400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:5839400-5839600	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr11:5839400-5839600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr11:5839400-5839600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr11:5839400-5839600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr11:5839400-5839600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:5839400-5839600	Enhancers	Liver	Liver
18	chr11:5839400-5839600	Active TSS	GM12878-XiMat	blood
19	chr11:5839400-5839800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr11:5839400-5839800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr11:5839400-5840400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr11:5839400-5840400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:5839400-5840400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr11:5839400-5840400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:5839600-5839800	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr11:5839600-5839800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr11:5839600-5839800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:5839600-5839800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr11:5839600-5839800	Flanking Active TSS	GM12878-XiMat	blood
30	chr11:5839600-5840000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:5839600-5840000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr11:5839600-5840000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr11:5839600-5840000	Flanking Active TSS	Liver	Liver
34	chr11:5839600-5840000	Active TSS	NHLF	lung
35	chr11:5839600-5840200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr11:5839600-5840200	Active TSS	Duodenum Mucosa	Duodenum
37	chr11:5839600-5840200	Flanking Active TSS	Dnd41	blood
38	chr11:5839600-5840400	Enhancers	Primary B cells from peripheral blood	blood
39	chr11:5839600-5840400	Enhancers	Primary T cells from cord blood	blood
40	chr11:5839600-5840400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr11:5839600-5840400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:5839600-5840400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:5839600-5840400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:5839800-5840000	Enhancers	Primary hematopoietic stem cells	blood
45	chr11:5839800-5840000	Active TSS	GM12878-XiMat	blood
46	chr11:5839800-5840200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:5839800-5840200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr11:5839800-5840200	Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr11:5839800-5840200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:5839800-5840200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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