Variant report

Variant	nsv549590
Chromosome Location	chr1:247494789-247495588
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:500)
CpG islands
(count:305)
Chromatin interactive
region (count:21)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:500 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr1:247495024-247495360	GM12878	blood:	n/a	n/a
2	BCL3	chr1:247494952-247495314	GM12878	blood:	n/a	chr1:247495254-247495263 chr1:247495200-247495209 chr1:247495255-247495268
3	BCLAF1	chr1:247494902-247495858	K562	blood:	n/a	chr1:247495606-247495615 chr1:247495387-247495400 chr1:247495254-247495263 chr1:247495395-247495408 chr1:247495607-247495620 chr1:247495603-247495616 chr1:247495200-247495209 chr1:247495642-247495655 chr1:247495381-247495390 chr1:247495626-247495639 chr1:247495255-247495268 chr1:247495371-247495384
4	BCLAF1	chr1:247495483-247495909	GM12878	blood:	n/a	chr1:247495606-247495615 chr1:247495607-247495620 chr1:247495603-247495616 chr1:247495642-247495655 chr1:247495626-247495639
5	BCLAF1	chr1:247494977-247495394	GM12878	blood:	n/a	chr1:247495254-247495263 chr1:247495200-247495209 chr1:247495381-247495390 chr1:247495255-247495268 chr1:247495371-247495384
6	BCLAF1	chr1:247494942-247495457	GM12878	blood:	n/a	chr1:247495387-247495400 chr1:247495254-247495263 chr1:247495395-247495408 chr1:247495200-247495209 chr1:247495381-247495390 chr1:247495255-247495268 chr1:247495371-247495384
7	BHLHE40	chr1:247495077-247495898	GM12878	blood:	n/a	chr1:247495605-247495621
8	BHLHE40	chr1:247494347-247496575	K562	blood:	n/a	chr1:247495605-247495621 chr1:247494560-247494576
9	BHLHE40	chr1:247495097-247495885	HepG2	liver:	n/a	chr1:247495605-247495621
10	BRCA1	chr1:247495106-247495317	Hela-S3	cervix:	n/a	n/a
11	CBX3	chr1:247495003-247497040	K562	blood:	n/a	n/a
12	CBX3	chr1:247494331-247494795	K562	blood:	n/a	n/a
13	CCNT2	chr1:247494234-247495919	K562	blood:	n/a	chr1:247495255-247495264
14	CEBPB	chr1:247495579-247495920	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr1:247495073-247495374	Hela-S3	cervix:	n/a	n/a
16	CEBPD	chr1:247494873-247495460	HepG2	liver:	n/a	n/a
17	CHD1	chr1:247495179-247496161	GM12878	blood:	n/a	n/a
18	CHD1	chr1:247493780-247497114	IMR90	lung:	n/a	n/a
19	CHD1	chr1:247494405-247494924	GM12878	blood:	n/a	n/a
20	CHD1	chr1:247494529-247495213	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD2	chr1:247495162-247495374	K562	blood:	n/a	n/a
22	CHD2	chr1:247494651-247494848	K562	blood:	n/a	n/a
23	CHD2	chr1:247495107-247495869	GM12878	blood:	n/a	n/a
24	CHD2	chr1:247495210-247495388	HepG2	liver:	n/a	n/a
25	CHD2	chr1:247494387-247494905	GM12878	blood:	n/a	n/a
26	CHD2	chr1:247494427-247495874	Hela-S3	cervix:	n/a	n/a
27	CREB1	chr1:247494888-247495855	A549	lung:	n/a	n/a
28	CREB1	chr1:247494145-247495875	HepG2	liver:	n/a	n/a
29	CTBP2	chr1:247494201-247495929	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr1:247495380-247495530	AG04449	skin:	n/a	n/a
31	CTCF	chr1:247495400-247495550	HRPEpiC	eye:	n/a	n/a
32	CTCF	chr1:247495340-247495490	SAEC	small airway:	n/a	n/a
33	CTCF	chr1:247495453-247495536	GM10248	blood:	n/a	n/a
34	CTCF	chr1:247495134-247495858	GM12878	blood:	n/a	n/a
35	CTCF	chr1:247494700-247494850	GM12865	blood:	n/a	n/a
36	CTCF	chr1:247495480-247495630	HAc	cerebellar:	n/a	n/a
37	CTCF	chr1:247495456-247495515	GM12892	blood:	n/a	n/a
38	CTCF	chr1:247494760-247494910	SAEC	small airway:	n/a	n/a
39	CTCF	chr1:247495432-247495780	K562	blood:	n/a	n/a
40	CTCF	chr1:247494482-247494829	K562	blood:	n/a	chr1:247494490-247494503
41	CTCF	chr1:247495400-247495550	AG09319	gingival:	n/a	n/a
42	CTCF	chr1:247495340-247495490	Caco-2	colon:	n/a	n/a
43	CTCF	chr1:247495438-247495521	GM10266	blood:	n/a	n/a
44	CTCF	chr1:247495432-247495504	GM19240	blood:	n/a	n/a
45	CTCF	chr1:247495440-247495590	GM12866	blood:	n/a	n/a
46	CTCF	chr1:247495060-247495210	GM12871	blood:	n/a	n/a
47	CTCF	chr1:247495380-247495530	GM12873	blood:	n/a	n/a
48	CTCF	chr1:247495420-247495570	GM12864	blood:	n/a	n/a
49	CTCF	chr1:247495360-247495510	HBMEC	blood vessel:	n/a	n/a
50	CTCF	chr1:247495458-247495496	GM13977	blood:	n/a	n/a

(count:305 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:247494926-247494976	HCT-116	colon:	n/a
2	chr1:247494767-247494817	NHDF-neo	bronchial:	n/a
3	chr1:247494767-247494817	HMEC	breast:	n/a
4	chr1:247495250-247495300	T-47D	breast:	n/a
5	chr1:247494926-247494976	ovcar-3	ovarian:	n/a
6	chr1:247494926-247494976	SK-N-SH_RA	brain:	n/a
7	chr1:247495212-247495262	HCPEpiC	choroid plexus:	n/a
8	chr1:247494767-247494817	NB4	blood:	n/a
9	chr1:247495250-247495300	H1-hESC	embryonic stem cell:	embryo
10	chr1:247494926-247494976	NB4	blood:	n/a
11	chr1:247494767-247494817	Hela-S3	cervix:	n/a
12	chr1:247495212-247495262	HepG2	liver:	n/a
13	chr1:247495250-247495300	ovcar-3	ovarian:	n/a
14	chr1:247494983-247495033	GM12892	blood:	n/a
15	chr1:247495212-247495262	T-47D	breast:	n/a
16	chr1:247494983-247495033	HEEpiC	esophagus:	n/a
17	chr1:247494983-247495033	HIPEpiC	eye:	n/a
18	chr1:247494926-247494976	GM12878	blood:	n/a
19	chr1:247495212-247495262	HIPEpiC	eye:	n/a
20	chr1:247494767-247494817	HEK293	kidney:	embryo
21	chr1:247495212-247495262	SAEC	small airway:	n/a
22	chr1:247495212-247495262	BJ	skin:	n/a
23	chr1:247494926-247494976	AG04450	lung:	fetal
24	chr1:247494767-247494817	A549	lung:	n/a
25	chr1:247495250-247495300	PANC-1	pancreas:	n/a
26	chr1:247494983-247495033	NH-A	brain:	n/a
27	chr1:247494767-247494817	SAEC	small airway:	n/a
28	chr1:247495250-247495300	SAEC	small airway:	n/a
29	chr1:247495212-247495262	AG09309	skin:	n/a
30	chr1:247494767-247494817	PFSK-1	brain:	n/a
31	chr1:247495212-247495262	NB4	blood:	n/a
32	chr1:247494926-247494976	SAEC	small airway:	n/a
33	chr1:247494926-247494976	HRE	kidney:	n/a
34	chr1:247494983-247495033	K562	blood:	n/a
35	chr1:247495250-247495300	PFSK-1	brain:	n/a
36	chr1:247495250-247495300	HEEpiC	esophagus:	n/a
37	chr1:247495212-247495262	HL-60	blood:	n/a
38	chr1:247494926-247494976	PANC-1	pancreas:	n/a
39	chr1:247495212-247495262	K562	blood:	n/a
40	chr1:247495250-247495300	NH-A	brain:	n/a
41	chr1:247494926-247494976	HepG2	liver:	n/a
42	chr1:247494983-247495033	GM06990	blood:	n/a
43	chr1:247494767-247494817	HCM	heart:	n/a
44	chr1:247495250-247495300	HCF	heart:	n/a
45	chr1:247495212-247495262	PrEC	prostate:	n/a
46	chr1:247494983-247495033	AG10803	skin:	n/a
47	chr1:247495212-247495262	Hela-S3	cervix:	n/a
48	chr1:247494926-247494976	GM19239	blood:	n/a
49	chr1:247495212-247495262	ProgFib	skin:	n/a
50	chr1:247494926-247494976	SK-N-MC	brain:	n/a

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247495212..247495870-chr7:102715654..102716186,2	Hela-S3	cervix:
2	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
3	chr1:247371399..247373319-chr1:247494315..247496686,3	K562	blood:
4	chr1:247371861..247375582-chr1:247493463..247496360,5	MCF-7	breast:
5	chr1:247495103..247495785-chr11:66056230..66056965,2	Hela-S3	cervix:
6	chr1:247495021..247495664-chr12:52444981..52445780,2	Hela-S3	cervix:
7	chr1:247373865..247374385-chr1:247494539..247495272,2	NB4	blood:
8	chr1:247266988..247268956-chr1:247494459..247496057,2	MCF-7	breast:
9	chr1:247495187..247495988-chr9:79008974..79009831,2	HCT-116	colon:
10	chr1:247473800..247482682-chr1:247490121..247498423,19	K562	blood:
11	chr1:247093791..247096097-chr1:247493835..247497465,5	K562	blood:
12	chr1:247093731..247095297-chr1:247494500..247497465,3	K562	blood:
13	chr1:247237656..247243483-chr1:247491762..247497969,8	K562	blood:
14	chr1:247494766..247495584-chr12:123849315..123850422,3	Hela-S3	cervix:
15	chr1:247371506..247373896-chr1:247494793..247496492,2	K562	blood:
16	chr1:247495202..247495979-chr14:105219028..105219965,2	Hela-S3	cervix:
17	chr1:247069586..247071786-chr1:247495195..247496702,2	K562	blood:
18	chr1:247495187..247496810-chr1:247522265..247524064,2	K562	blood:
19	chr1:247495432..247495974-chr10:77162497..77163288,2	Hela-S3	cervix:
20	chr1:247495232..247496940-chr1:247645349..247647027,2	K562	blood:
21	chr1:247484098..247486215-chr1:247495440..247497543,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NLRP3-1	chr1:247495187-247498708	NONHSAT010771
2	lnc-NLRP3-1	chr1:247495531-247495666	NONHSAT010772

No data

Variant related genes	Relation type
ZNF496	TF binding region
ZNF496	CpG island
ENSG00000162714	chromatin interactions
ENSG00000153207	chromatin interactions
ENSG00000135002	chromatin interactions
ENSG00000237149	chromatin interactions
ENSG00000174851	chromatin interactions
ENSG00000184990	chromatin interactions
ENSG00000188295	chromatin interactions
ENSG00000227671	chromatin interactions
ENSG00000139697	chromatin interactions
ENSG00000256092	chromatin interactions
ENSG00000135747	chromatin interactions
ENSG00000123358	chromatin interactions

Extended variants
information (count: 19 )
Associated
traits (count: 30 )

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570090484	chr1:247494847-247494848	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
2	rs537509760	chr1:247494874-247494875	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
3	rs552690857	chr1:247494879-247494880	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
4	rs181944724	chr1:247494911-247494912	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
5	rs535783985	chr1:247494947-247494948	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
6	rs207461402	chr1:247494960-247494961	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
7	rs534904915	chr1:247494979-247494980	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
8	rs553572259	chr1:247494992-247494993	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
9	rs574992625	chr1:247495028-247495029	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
10	rs111800993	chr1:247495038-247495039	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
11	rs185949927	chr1:247495099-247495100	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
12	rs535766669	chr1:247495264-247495265	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	Overlapped CNVs	n/a
13	rs554110229	chr1:247495354-247495355	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	12 gene(s)	Overlapped CNVs	n/a
14	rs113566032	chr1:247495385-247495386	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	12 gene(s)	Overlapped CNVs	n/a
15	rs141676081	chr1:247495390-247495391	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	12 gene(s)	Overlapped CNVs	n/a
16	rs564824139	chr1:247495414-247495415	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	12 gene(s)	Overlapped CNVs	n/a
17	rs576910624	chr1:247495510-247495511	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	13 gene(s)	Overlapped CNVs	n/a
18	rs572052400	chr1:247495514-247495515	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	13 gene(s)	Overlapped CNVs	n/a
19	rs540825373	chr1:247495553-247495554	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	13 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:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247493400-247494800	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr1:247493600-247496400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:247493800-247495400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr1:247493800-247495800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:247493800-247496200	Active TSS	HSMMtube	muscle
6	chr1:247493800-247496400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:247493800-247496600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:247494000-247494800	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr1:247494000-247495000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr1:247494000-247495000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:247494000-247496000	Active TSS	NHLF	lung
12	chr1:247494000-247496400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:247494000-247496400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:247494000-247496400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:247494000-247496400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:247494000-247496400	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:247494000-247496400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:247494000-247496600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:247494000-247496600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:247494200-247494800	Enhancers	Fetal Brain Male	brain
21	chr1:247494200-247494800	Bivalent/Poised TSS	HepG2	liver
22	chr1:247494200-247495000	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr1:247494200-247495000	Active TSS	Stomach Mucosa	stomach
24	chr1:247494200-247495600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:247494200-247495600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:247494200-247495600	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr1:247494200-247495600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:247494200-247495600	Active TSS	GM12878-XiMat	blood
29	chr1:247494200-247495600	Active TSS	HMEC	breast
30	chr1:247494200-247495800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:247494200-247495800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr1:247494200-247495800	Active TSS	Brain Angular Gyrus	brain
33	chr1:247494200-247495800	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr1:247494200-247495800	Active TSS	Brain Substantia Nigra	brain
35	chr1:247494200-247495800	Active TSS	Fetal Intestine Large	intestine
36	chr1:247494200-247495800	Active TSS	Fetal Lung	lung
37	chr1:247494200-247495800	Active TSS	Fetal Stomach	stomach
38	chr1:247494200-247495800	Active TSS	Fetal Thymus	thymus
39	chr1:247494200-247495800	Active TSS	Psoas Muscle	Psoas
40	chr1:247494200-247495800	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr1:247494200-247495800	Active TSS	Thymus	Thymus
42	chr1:247494200-247495800	Active TSS	Hela-S3	cervix
43	chr1:247494200-247495800	Active TSS	HUVEC	blood vessel
44	chr1:247494200-247495800	Active TSS	K562	blood
45	chr1:247494200-247495800	Active TSS	NHDF-Ad	bronchial
46	chr1:247494200-247495800	Active TSS	NHEK	skin
47	chr1:247494200-247496000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:247494200-247496000	Active TSS	Brain Anterior Caudate	brain
49	chr1:247494200-247496000	Active TSS	Fetal Brain Female	brain
50	chr1:247494200-247496000	Active TSS	Rectal Smooth Muscle	rectum

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