Variant report

Variant	rs556478971
Chromosome Location	chr9:98637713-98637714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:495)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:495 , 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	MAX	chr9:98637238-98638478	HepG2	liver:	n/a	n/a
2	EGR1	chr9:98637052-98638446	ECC-1	luminal epithelium:	n/a	chr9:98637320-98637334
3	POLR2A	chr9:98636530-98639513	GM12878	blood:	n/a	n/a
4	SP1	chr9:98637683-98638497	H1-hESC	embryonic stem cell:	n/a	chr9:98638158-98638169
5	JUND	chr9:98637122-98638693	K562	blood:	n/a	n/a
6	YY1	chr9:98637708-98638458	K562	blood:	n/a	n/a
7	SMARCB1	chr9:98637163-98638588	Hela-S3	cervix:	n/a	n/a
8	BCLAF1	chr9:98636979-98638715	GM12878	blood:	n/a	chr9:98638264-98638273
9	POLR2A	chr9:98637515-98638482	HepG2	liver:	n/a	n/a
10	GATA3	chr9:98637427-98638817	MCF-7	breast:	n/a	n/a
11	POLR2A	chr9:98636741-98638700	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:98637433-98638590	H1-hESC	embryonic stem cell:	n/a	n/a
13	RUNX3	chr9:98636942-98638662	GM12878	blood:	n/a	n/a
14	POLR2A	chr9:98637208-98638679	MCF-7	breast:	n/a	n/a
15	HA-E2F1	chr9:98637052-98638724	MCF-7	breast:	n/a	n/a
16	USF1	chr9:98637693-98638591	A549	lung:	n/a	n/a
17	GATA3	chr9:98637486-98638620	SK-N-SH	brain:	n/a	n/a
18	RELA	chr9:98637107-98638666	GM15510	blood:	n/a	n/a
19	MEF2A	chr9:98637440-98638608	GM12878	blood:	n/a	n/a
20	TAF1	chr9:98637590-98638559	GM12891	blood:	n/a	n/a
21	TAF1	chr9:98637162-98638776	MCF-7	breast:	n/a	n/a
22	MTA3	chr9:98636949-98639183	GM12878	blood:	n/a	n/a
23	TBP	chr9:98636911-98639299	Hela-S3	cervix:	n/a	n/a
24	SIN3A	chr9:98636789-98638787	H1-hESC	embryonic stem cell:	n/a	n/a
25	ATF2	chr9:98637199-98638494	GM12878	blood:	n/a	n/a
26	STAT5A	chr9:98637637-98638554	K562	blood:	n/a	n/a
27	KAP1	chr9:98637026-98638612	U2OS	brain:	n/a	n/a
28	POLR2A	chr9:98636707-98638697	K562	blood:	n/a	n/a
29	POLR2A	chr9:98636660-98638576	HepG2	liver:	n/a	n/a
30	TBP	chr9:98637030-98638868	GM12878	blood:	n/a	n/a
31	SIN3AK20	chr9:98637289-98638927	MCF-7	breast:	n/a	n/a
32	REST	chr9:98637424-98638474	SK-N-SH	brain:	n/a	n/a
33	CHD1	chr9:98637262-98639223	GM12878	blood:	n/a	n/a
34	POLR2A	chr9:98637444-98638569	PANC-1	pancreas:	n/a	n/a
35	CREB1	chr9:98637559-98638606	K562	blood:	n/a	n/a
36	RELA	chr9:98637070-98638617	GM18951	blood:	n/a	n/a
37	FOS	chr9:98637695-98637973	MCF10A-Er-Src	breast:	n/a	n/a
38	ZBTB33	chr9:98637520-98638397	K562	blood:	n/a	n/a
39	TEAD4	chr9:98637511-98638580	HepG2	liver:	n/a	n/a
40	HMGN3	chr9:98637207-98638572	K562	blood:	n/a	n/a
41	SIN3AK20	chr9:98637562-98638028	PFSK-1	brain:	n/a	n/a
42	RCOR1	chr9:98637284-98638606	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr9:98637160-98638682	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr9:98637053-98638757	Raji	blood:	n/a	n/a
45	POLR2A	chr9:98636937-98638754	K562	blood:	n/a	n/a
46	POLR2A	chr9:98637479-98638636	GM12878	blood:	n/a	n/a
47	EP300	chr9:98637690-98638541	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF12	chr9:98637509-98638591	GM12878	blood:	n/a	n/a
49	ELF1	chr9:98637459-98638608	GM12878	blood:	n/a	chr9:98637959-98637972
50	SPI1	chr9:98637709-98637919	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:98270649..98275167-chr9:98636318..98639773,5	MCF-7	breast:
2	chr7:30518092..30518790-chr9:98637529..98638155,2	MCF-7	breast:
3	chr9:98637191..98639517-chr9:98666345..98668961,2	MCF-7	breast:
4	chr9:98636376..98639087-chr9:98667887..98670748,3	MCF-7	breast:
5	chr9:98637661..98638446-chrX:118602263..118602952,2	Hela-S3	cervix:
6	chr9:98637084..98640693-chr9:98667295..98670393,4	K562	blood:
7	chr5:131629322..131630937-chr9:98636920..98639534,2	MCF-7	breast:
8	chr9:98276862..98280186-chr9:98636651..98639407,3	K562	blood:
9	chr17:56736371..56738298-chr9:98637681..98639486,2	MCF-7	breast:
10	chr9:98636162..98639165-chr9:98683503..98686735,3	MCF-7	breast:
11	chr1:67896089..67896845-chr9:98637353..98638274,2	Hela-S3	cervix:
12	chr9:98534328..98536116-chr9:98636365..98638226,2	MCF-7	breast:
13	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
14	chr9:98277796..98280674-chr9:98636940..98639822,3	K562	blood:
15	chr1:155657851..155658412-chr9:98637639..98638211,2	Hela-S3	cervix:
16	chr9:98636137..98638134-chr9:98783030..98785648,2	K562	blood:
17	chr9:98078160..98080305-chr9:98637483..98639375,2	MCF-7	breast:
18	chr9:98636642..98639611-chr9:98680367..98683270,2	K562	blood:
19	chr9:98637678..98640109-chr9:98685155..98688009,2	K562	blood:
20	chr6:10415020..10415709-chr9:98637686..98638605,2	Hela-S3	cervix:
21	chr9:98188917..98190953-chr9:98637709..98639661,2	MCF-7	breast:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-3	chr9:98637262-98638258	ENSG00000175611
2	lnc-PTCH1-3	chr9:98637262-98637869	ENSG00000175611
3	lnc-PTCH1-3	chr9:98637262-98637762	ENSG00000175611
4	lnc-PTCH1-3	chr9:98637262-98638259	NONHSAT133402
5	lnc-PTCH1-3	chr9:98637262-98638394	NONHSAT133403
6	lnc-PTCH1-3	chr9:98637508-98638366	NONHSAT133404
7	lnc-PTCH1-3	chr9:98637262-98637762	ENSG00000175611.7

No data

Variant related genes	Relation type
LINC00476	TF binding region
ERCC6L2	TF binding region
ENSG00000199202	Chromatin interaction
ENSG00000005022	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000237857	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000197208	Chromatin interaction
ENSG00000163374	Chromatin interaction
ENSG00000106100	Chromatin interaction
ENSG00000142864	Chromatin interaction
ENSG00000252847	Chromatin interaction
ENSG00000225194	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000268926	Chromatin interaction
ENSG00000137203	Chromatin interaction
ENSG00000237631	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv524894	chr9:98637430-98640244	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98636400-98639200	Active TSS	NHLF	lung
2	chr9:98636400-98639600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr9:98636400-98639600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:98636400-98639800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr9:98636600-98637800	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr9:98636600-98638800	ZNF genes & repeats	Fetal Brain Male	brain
7	chr9:98636600-98639400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:98636600-98639800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:98636600-98639800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:98636600-98640000	Active TSS	A549	lung
11	chr9:98636800-98638800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:98636800-98639000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:98636800-98639000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:98636800-98639000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:98636800-98639200	Active TSS	Aorta	Aorta
16	chr9:98636800-98639400	Active TSS	Ovary	ovary
17	chr9:98636800-98639400	Active TSS	Right Ventricle	heart
18	chr9:98637000-98638800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr9:98637000-98638800	Active TSS	Gastric	stomach
20	chr9:98637000-98638800	Active TSS	Lung	lung
21	chr9:98637000-98638800	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr9:98637000-98638800	Active TSS	Small Intestine	intestine
23	chr9:98637000-98639000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr9:98637000-98639000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr9:98637000-98639000	Active TSS	Thymus	Thymus
26	chr9:98637000-98639200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr9:98637000-98639200	Active TSS	GM12878-XiMat	blood
28	chr9:98637000-98639400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:98637000-98639400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:98637000-98639400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:98637000-98639400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:98637000-98639400	Active TSS	Fetal Muscle Trunk	muscle
33	chr9:98637000-98639400	Active TSS	NHDF-Ad	bronchial
34	chr9:98637000-98639600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:98637000-98639800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr9:98637000-98639800	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr9:98637000-98640400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:98637200-98638600	Active TSS	Primary hematopoietic stem cells	blood
39	chr9:98637200-98638600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr9:98637200-98638600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:98637200-98638600	Active TSS	Brain Angular Gyrus	brain
42	chr9:98637200-98638600	Active TSS	Colon Smooth Muscle	Colon
43	chr9:98637200-98638600	Active TSS	Spleen	Spleen
44	chr9:98637200-98638800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:98637200-98638800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:98637200-98638800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:98637200-98638800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr9:98637200-98638800	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr9:98637200-98638800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:98637200-98638800	Active TSS	Brain Anterior Caudate	brain

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