Variant report

Variant	nsv549587
Chromosome Location	chr1:247400259-247438446
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	chr1:247429372-247429524	K562	blood:	n/a	n/a
2	BHLHE40	chr1:247423757-247423954	HepG2	liver:	n/a	n/a
3	CBX3	chr1:247409665-247409988	K562	blood:	n/a	n/a
4	CBX3	chr1:247409672-247409965	K562	blood:	n/a	n/a
5	CEBPB	chr1:247407042-247407310	IMR90	lung:	n/a	chr1:247407201-247407218
6	CEBPB	chr1:247432412-247432635	HepG2	liver:	n/a	n/a
7	CTCF	chr1:247431831-247431923	HepG2	liver:	n/a	n/a
8	CTCF	chr1:247431760-247431910	HVMF	connective:	n/a	n/a
9	CTCF	chr1:247431860-247432010	HCM	heart:	n/a	n/a
10	CTCF	chr1:247431820-247431970	HCPEpiC	choroid plexus:	n/a	n/a
11	CTCF	chr1:247427976-247427994	Kidney_OC	kidney:	n/a	n/a
12	CTCF	chr1:247431800-247431950	AG04450	lung:	n/a	n/a
13	CTCF	chr1:247431860-247432010	HCPEpiC	choroid plexus:	n/a	n/a
14	CTCF	chr1:247431811-247431944	K562	blood:	n/a	n/a
15	CTCF	chr1:247438280-247438430	GM12872	blood:	n/a	n/a
16	CTCF	chr1:247406299-247406306	GM13976	blood:	n/a	n/a
17	CTCF	chr1:247431780-247431930	HPAF	blood vessel:	n/a	n/a
18	CTCF	chr1:247432900-247433050	K562	blood:	n/a	n/a
19	CTCF	chr1:247402000-247402150	GM12867	blood:	n/a	n/a
20	CTCF	chr1:247431780-247431930	HMF	breast:	n/a	n/a
21	CTCF	chr1:247431798-247431929	HepG2	liver:	n/a	n/a
22	CTCF	chr1:247431820-247431970	HMF	breast:	n/a	n/a
23	CTCF	chr1:247432920-247433070	HepG2	liver:	n/a	n/a
24	CTCF	chr1:247431780-247431930	HVMF	connective:	n/a	n/a
25	CTCF	chr1:247431860-247432010	AG09309	skin:	n/a	n/a
26	CTCF	chr1:247431841-247431977	K562	blood:	n/a	n/a
27	CTCF	chr1:247431846-247431912	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr1:247421304-247421361	LNCaP	prostate:	n/a	n/a
29	EP300	chr1:247429553-247429570	K562	blood:	n/a	n/a
30	FAM48A	chr1:247422798-247422842	GM12878	blood:	n/a	n/a
31	FOS	chr1:247405063-247405397	MCF10A-Er-Src	breast:	n/a	chr1:247405202-247405214 chr1:247405203-247405213 chr1:247405205-247405216 chr1:247405203-247405213 chr1:247405204-247405212 chr1:247405203-247405213 chr1:247405203-247405213 chr1:247405204-247405211 chr1:247405204-247405212
32	FOS	chr1:247405053-247405389	MCF10A-Er-Src	breast:	n/a	chr1:247405202-247405214 chr1:247405203-247405213 chr1:247405205-247405216 chr1:247405203-247405213 chr1:247405204-247405212 chr1:247405203-247405213 chr1:247405203-247405213 chr1:247405204-247405211 chr1:247405204-247405212
33	FOS	chr1:247405048-247405396	MCF10A-Er-Src	breast:	n/a	chr1:247405202-247405214 chr1:247405203-247405213 chr1:247405205-247405216 chr1:247405203-247405213 chr1:247405204-247405212 chr1:247405203-247405213 chr1:247405203-247405213 chr1:247405204-247405211 chr1:247405204-247405212
34	FOS	chr1:247405035-247405390	MCF10A-Er-Src	breast:	n/a	chr1:247405202-247405214 chr1:247405203-247405213 chr1:247405205-247405216 chr1:247405203-247405213 chr1:247405204-247405212 chr1:247405203-247405213 chr1:247405203-247405213 chr1:247405204-247405211 chr1:247405204-247405212
35	FOSL2	chr1:247405107-247405336	SK-N-SH	brain:	n/a	chr1:247405202-247405214 chr1:247405203-247405213 chr1:247405205-247405216 chr1:247405203-247405213 chr1:247405204-247405212 chr1:247405203-247405213 chr1:247405203-247405213 chr1:247405204-247405211 chr1:247405204-247405212
36	FOSL2	chr1:247438256-247438549	HepG2	liver:	n/a	n/a
37	FOSL2	chr1:247429334-247429742	SK-N-SH	brain:	n/a	n/a
38	FOXA1	chr1:247438179-247438586	HepG2	liver:	n/a	n/a
39	FOXA2	chr1:247432089-247432276	HepG2	liver:	n/a	n/a
40	IRF1	chr1:247409825-247409970	K562	blood:	n/a	n/a
41	KAP1	chr1:247409624-247410053	K562	blood:	n/a	n/a
42	KAP1	chr1:247433307-247433545	HEK293	kidney:	n/a	n/a
43	MAFF	chr1:247438181-247438502	HepG2	liver:	n/a	n/a
44	MAFK	chr1:247438155-247438540	HepG2	liver:	n/a	n/a
45	MAFK	chr1:247438187-247438528	HepG2	liver:	n/a	n/a
46	MAFK	chr1:247400780-247400993	HepG2	liver:	n/a	n/a
47	MAFK	chr1:247400773-247400967	HepG2	liver:	n/a	n/a
48	MYC	chr1:247422726-247422755	MCF10A-Er-Src	breast:	n/a	n/a
49	MYC	chr1:247405131-247405407	MCF10A-Er-Src	breast:	n/a	n/a
50	PBX3	chr1:247429367-247429792	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:247420421-247420471	HCF	heart:	n/a
2	chr1:247420421-247420471	IMR90	lung:	fetal
3	chr1:247420421-247420471	AG04450	lung:	fetal
4	chr1:247418074-247418124	U87	brain:	n/a
5	chr1:247418074-247418124	SKMC	muscle:	n/a
6	chr1:247418074-247418124	HL-60	blood:	n/a
7	chr1:247418074-247418124	HCF	heart:	n/a
8	chr1:247420421-247420471	HRPEpiC	eye:	n/a
9	chr1:247418074-247418124	HCPEpiC	choroid plexus:	n/a
10	chr1:247418074-247418124	SK-N-MC	brain:	n/a
11	chr1:247420421-247420471	K562	blood:	n/a
12	chr1:247420421-247420471	ovcar-3	ovarian:	n/a
13	chr1:247418074-247418124	LNCaP	prostate:	n/a
14	chr1:247418074-247418124	CMK	blood:	n/a
15	chr1:247418074-247418124	IMR90	lung:	fetal
16	chr1:247418074-247418124	Hela-S3	cervix:	n/a
17	chr1:247418074-247418124	SAEC	small airway:	n/a
18	chr1:247420421-247420471	HCM	heart:	n/a
19	chr1:247418074-247418124	HMEC	breast:	n/a
20	chr1:247420421-247420471	GM12892	blood:	n/a
21	chr1:247420421-247420471	SK-N-MC	brain:	n/a
22	chr1:247420421-247420471	HIPEpiC	eye:	n/a
23	chr1:247418074-247418124	GM12878	blood:	n/a
24	chr1:247418074-247418124	K562	blood:	n/a
25	chr1:247420421-247420471	HRE	kidney:	n/a
26	chr1:247418074-247418124	NT2-D1	testis:	n/a
27	chr1:247420421-247420471	HPAEpiC	pulmonary alveolar:	n/a
28	chr1:247420421-247420471	PANC-1	pancreas:	n/a
29	chr1:247418074-247418124	ECC-1	luminal epithelium:	n/a
30	chr1:247420421-247420471	NH-A	brain:	n/a
31	chr1:247420421-247420471	PFSK-1	brain:	n/a
32	chr1:247418074-247418124	NH-A	brain:	n/a
33	chr1:247418074-247418124	GM12891	blood:	n/a
34	chr1:247420421-247420471	HNPCEpiC	eye:	n/a
35	chr1:247418074-247418124	HNPCEpiC	eye:	n/a
36	chr1:247418074-247418124	HRCEpiC	kidney:	n/a
37	chr1:247420421-247420471	HL-60	blood:	n/a
38	chr1:247420421-247420471	Hela-S3	cervix:	n/a
39	chr1:247418074-247418124	HEEpiC	esophagus:	n/a
40	chr1:247418074-247418124	GM19239	blood:	n/a
41	chr1:247420421-247420471	U87	brain:	n/a
42	chr1:247420421-247420471	HepG2	liver:	n/a
43	chr1:247420421-247420471	BE2_C	brain:	n/a
44	chr1:247420421-247420471	HEEpiC	esophagus:	n/a
45	chr1:247418074-247418124	AG04449	skin:	fetal
46	chr1:247418074-247418124	H1-hESC	embryonic stem cell:	embryo
47	chr1:247418074-247418124	PANC-1	pancreas:	n/a
48	chr1:247420421-247420471	MCF10A-Er-Src	breast:	n/a
49	chr1:247418074-247418124	MCF-7	breast:	n/a
50	chr1:247420421-247420471	Hepatocyte	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:247397665..247399699-chr1:247438222..247441070,2	K562	blood:
2	chr1:247392601..247395028-chr1:247403697..247405933,2	K562	blood:
3	chr1:247392297..247394104-chr1:247407424..247409798,2	K562	blood:
4	chr1:247370277..247372519-chr1:247432525..247434040,2	K562	blood:
5	chr1:247275409..247277041-chr1:247418740..247421372,2	K562	blood:
6	chr1:247395920..247398190-chr1:247413415..247415591,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF124-2	chr1:247405079-247405125	ENSG00000232347.1

Variant related genes	Relation type
ENSG00000232347	TF binding region
VN1R5	TF binding region
VN1R17P	TF binding region
ENSG00000232347	CpG island
VN1R5	CpG island
VN1R17P	CpG island
ENSG00000221953	chromatin interactions
ENSG00000214144	chromatin interactions

Extended variants
information (count: 652 )
Associated
traits (count: 30 )

Variant overlapped rSNPs/rCNVs (count:652 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543649974	chr1:247402043-247402044	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs186543767	chr1:247402109-247402110	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs544265265	chr1:247403755-247403756	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs9426224	chr1:247403765-247403766	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs9426173	chr1:247403766-247403767	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	mRNA abundance
6	rs545501840	chr1:247403771-247403772	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs560631721	chr1:247403787-247403788	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs192344128	chr1:247403820-247403821	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs201576295	chr1:247403857-247403858	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs561547959	chr1:247403908-247403909	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs142340777	chr1:247403919-247403920	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	mRNA abundance
12	rs550276034	chr1:247403923-247403924	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs531753097	chr1:247403991-247403992	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs539120760	chr1:247404242-247404243	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs10754540	chr1:247404268-247404269	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs566276341	chr1:247404279-247404280	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs533727921	chr1:247404323-247404324	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs555178033	chr1:247404432-247404433	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs2793290	chr1:247404457-247404458	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs538164041	chr1:247404469-247404470	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs2793291	chr1:247404481-247404482	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs577979725	chr1:247404487-247404488	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs545127111	chr1:247404500-247404501	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs554307487	chr1:247404545-247404546	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs572604965	chr1:247404547-247404548	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs543220421	chr1:247404593-247404594	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs561485688	chr1:247404611-247404612	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs547810940	chr1:247404647-247404648	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs193170491	chr1:247404653-247404654	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs184686996	chr1:247404668-247404669	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs34058820	chr1:247404739-247404740	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs199800885	chr1:247404741-247404742	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs11581201	chr1:247404767-247404768	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs74805327	chr1:247404768-247404769	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs147750413	chr1:247404786-247404787	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs370810115	chr1:247404831-247404832	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs2793292	chr1:247404853-247404854	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs368361906	chr1:247404879-247404880	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs12118988	chr1:247404911-247404912	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs527413950	chr1:247405022-247405023	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs142602289	chr1:247405068-247405069	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs189961260	chr1:247405072-247405073	Inactive region	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs555616281	chr1:247405114-247405115	Inactive region	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs146777673	chr1:247405163-247405164	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs374426987	chr1:247405164-247405165	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs556426992	chr1:247405189-247405190	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs571501250	chr1:247405218-247405219	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs556820383	chr1:247405224-247405225	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs112223064	chr1:247405225-247405226	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs570697376	chr1:247405236-247405237	Inactive region	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:30)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Cancer	17060936	CNVD
Multiple myeloma	16616336	CNVD
Cutaneous malignant melanoma	18794153	CNVD
Astrocytoma	17934521	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Breast cancer	20409316	CNVD
Fibroblasts	17951408	CNVD
Lung cancer	17951408	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247407000-247407200	Enhancers	K562	blood
2	chr1:247409000-247409400	ZNF genes & repeats	Aorta	Aorta
3	chr1:247416200-247419600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:247419400-247420000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:247419400-247420000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:247419600-247420000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr1:247419600-247420000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:247419600-247420000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:247419600-247420000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:247419600-247420000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:247419600-247420200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:247429200-247429600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:247429600-247429800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:247430000-247432200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:247432000-247432200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:247432000-247433200	Enhancers	HepG2	liver
17	chr1:247432200-247432800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:247432200-247433200	Enhancers	Gastric	stomach
19	chr1:247432200-247433600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:247432800-247433600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:247433600-247436400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:247433600-247436600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:247435200-247435400	Enhancers	Fetal Kidney	kidney
24	chr1:247435400-247436000	Weak transcription	Fetal Kidney	kidney
25	chr1:247436000-247436400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:247436000-247436400	Enhancers	HSMMtube	muscle
27	chr1:247436000-247436800	Enhancers	Fetal Kidney	kidney
28	chr1:247436000-247436800	Enhancers	Fetal Muscle Leg	muscle
29	chr1:247436000-247436800	Enhancers	Placenta	Placenta
30	chr1:247436200-247436800	Enhancers	Psoas Muscle	Psoas
31	chr1:247436200-247436800	Enhancers	HSMM	muscle
32	chr1:247436200-247437000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:247436400-247436600	Enhancers	Gastric	stomach
34	chr1:247436400-247436800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:247436400-247436800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:247436400-247436800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:247436400-247436800	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:247436400-247436800	Enhancers	Spleen	Spleen
39	chr1:247436400-247436800	Flanking Active TSS	HSMMtube	muscle
40	chr1:247436400-247437000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr1:247436400-247437000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:247436400-247437000	Enhancers	Brain Cingulate Gyrus	brain
43	chr1:247436400-247437000	Enhancers	Fetal Heart	heart
44	chr1:247436600-247436800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:247436600-247437000	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr1:247436600-247437000	Enhancers	Brain Substantia Nigra	brain
47	chr1:247436600-247438000	Weak transcription	Gastric	stomach
48	chr1:247436800-247437000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:247436800-247437200	Active TSS	Brain Angular Gyrus	brain
50	chr1:247436800-247438000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links