Variant report

Variant	rs73527759
Chromosome Location	chr9:98278940-98278941
allele	C/G
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	MAX	chr9:98278886-98279397	SK-N-SH	brain:	n/a	n/a
2	HMGN3	chr9:98278029-98279519	K562	blood:	n/a	n/a
3	E2F6	chr9:98278909-98279465	K562	blood:	n/a	chr9:98279407-98279419 chr9:98279410-98279419
4	RCOR1	chr9:98278116-98279554	K562	blood:	n/a	n/a
5	TAF1	chr9:98278934-98279256	K562	blood:	n/a	n/a
6	MAX	chr9:98278497-98279544	A549	lung:	n/a	n/a
7	MXI1	chr9:98277534-98279666	SK-N-SH	brain:	n/a	n/a
8	ZC3H11A	chr9:98278777-98278968	K562	blood:	n/a	n/a
9	ATF3	chr9:98278932-98279368	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F4	chr9:98278887-98279396	MCF10A-Er-Src	breast:	n/a	n/a
11	EGR1	chr9:98278830-98279576	K562	blood:	n/a	chr9:98279412-98279421 chr9:98279406-98279428 chr9:98279411-98279421 chr9:98279411-98279424 chr9:98279412-98279422 chr9:98279409-98279419 chr9:98279410-98279425 chr9:98279412-98279423 chr9:98279410-98279424 chr9:98279411-98279424 chr9:98279412-98279422 chr9:98279405-98279418 chr9:98279411-98279424 chr9:98279411-98279424
12	JUND	chr9:98278707-98279476	K562	blood:	n/a	chr9:98279347-98279356
13	USF1	chr9:98278929-98279388	A549	lung:	n/a	chr9:98279149-98279160
14	USF2	chr9:98278873-98279346	H1-hESC	embryonic stem cell:	n/a	chr9:98279149-98279160
15	RAD21	chr9:98278595-98278949	SK-N-SH_RA	brain:	n/a	n/a
16	MAX	chr9:98278903-98279629	H1-hESC	embryonic stem cell:	n/a	n/a
17	USF1	chr9:98278929-98279273	A549	lung:	n/a	chr9:98279149-98279160
18	MAZ	chr9:98278011-98279894	IMR90	lung:	n/a	n/a
19	USF1	chr9:98278903-98279351	ECC-1	luminal epithelium:	n/a	chr9:98279149-98279160
20	USF1	chr9:98278764-98279501	HCT-116	colon:	n/a	chr9:98279149-98279160
21	MAX	chr9:98278551-98279435	K562	blood:	n/a	n/a
22	MAX	chr9:98278686-98279405	ECC-1	luminal epithelium:	n/a	n/a
23	UBTF	chr9:98278330-98279500	K562	blood:	n/a	n/a
24	E2F6	chr9:98278671-98279413	A549	lung:	n/a	chr9:98278681-98278690
25	ELF1	chr9:98278937-98279363	GM12878	blood:	n/a	n/a
26	POLR2A	chr9:98278908-98279405	K562	blood:	n/a	n/a
27	MAX	chr9:98278549-98279426	ECC-1	luminal epithelium:	n/a	n/a
28	REST	chr9:98277262-98280262	H1-neurons	neurons:	n/a	chr9:98277674-98277692 chr9:98277673-98277693 chr9:98278638-98278651 chr9:98277673-98277693
29	USF1	chr9:98278904-98279486	H1-hESC	embryonic stem cell:	n/a	chr9:98279149-98279160
30	SIN3A	chr9:98277461-98280031	H1-hESC	embryonic stem cell:	n/a	n/a
31	USF1	chr9:98278867-98279455	SK-N-SH	brain:	n/a	chr9:98279149-98279160
32	MAZ	chr9:98278083-98279519	K562	blood:	n/a	n/a
33	RAD21	chr9:98278688-98279757	IMR90	lung:	n/a	chr9:98279444-98279453
34	ZNF384	chr9:98278810-98279450	K562	blood:	n/a	n/a
35	TCF12	chr9:98278668-98279142	A549	lung:	n/a	n/a
36	MYC	chr9:98278137-98279422	K562	blood:	n/a	n/a
37	EGR1	chr9:98278926-98279545	K562	blood:	n/a	chr9:98279412-98279421 chr9:98279406-98279428 chr9:98279411-98279421 chr9:98279411-98279424 chr9:98279412-98279422 chr9:98279409-98279419 chr9:98279410-98279425 chr9:98279412-98279423 chr9:98279410-98279424 chr9:98279411-98279424 chr9:98279412-98279422 chr9:98279405-98279418 chr9:98279411-98279424 chr9:98279411-98279424
38	POLR2A	chr9:98278884-98279395	K562	blood:	n/a	n/a
39	FOXA1	chr9:98278940-98279475	HepG2	liver:	n/a	chr9:98279241-98279256 chr9:98279202-98279217
40	USF1	chr9:98278870-98279461	K562	blood:	n/a	chr9:98279149-98279160
41	UBTF	chr9:98278058-98279590	K562	blood:	n/a	n/a
42	TAF1	chr9:98278924-98280059	H1-neurons	neurons:	n/a	n/a
43	MAX	chr9:98278550-98279565	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTBP2	chr9:98278676-98280022	H1-hESC	embryonic stem cell:	n/a	n/a
45	E2F6	chr9:98278064-98279498	K562	blood:	n/a	chr9:98278094-98278101 chr9:98278391-98278406 chr9:98278681-98278690 chr9:98278094-98278101 chr9:98278094-98278101 chr9:98279407-98279419 chr9:98279410-98279419
46	FOXA1	chr9:98278930-98279437	HepG2	liver:	n/a	chr9:98279241-98279256 chr9:98279202-98279217
47	BACH1	chr9:98278836-98279643	H1-hESC	embryonic stem cell:	n/a	n/a
48	EGR1	chr9:98278902-98279595	ECC-1	luminal epithelium:	n/a	chr9:98279412-98279421 chr9:98279406-98279428 chr9:98279411-98279421 chr9:98279411-98279424 chr9:98279412-98279422 chr9:98279409-98279419 chr9:98279410-98279425 chr9:98279412-98279423 chr9:98279410-98279424 chr9:98279411-98279424 chr9:98279412-98279422 chr9:98279405-98279418 chr9:98279411-98279424 chr9:98279411-98279424
49	RAD21	chr9:98278904-98280100	H1-hESC	embryonic stem cell:	n/a	chr9:98279444-98279453
50	USF1	chr9:98278874-98279318	A549	lung:	n/a	chr9:98279149-98279160

No.	Distal block	Cell Line	Cell type
1	chr9:98276862..98280186-chr9:98636651..98639407,3	K562	blood:
2	chr9:98277796..98280674-chr9:98636940..98639822,3	K562	blood:
3	chr9:98078194..98081816-chr9:98277777..98279552,3	K562	blood:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000175611	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs28509458	0.82[AFR][1000 genomes]
rs28687112	0.82[AFR][1000 genomes]
rs28753971	0.92[AFR][1000 genomes]
rs58490443	0.83[AFR][1000 genomes]
rs60008840	0.87[AFR][1000 genomes]
rs60031743	0.84[AFR][1000 genomes]
rs61184807	0.87[AFR][1000 genomes]
rs73527757	0.91[AFR][1000 genomes]
rs73527766	0.97[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98274600-98279600	Active TSS	Duodenum Mucosa	Duodenum
2	chr9:98277200-98279000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
3	chr9:98277200-98280000	Active TSS	Fetal Kidney	kidney
4	chr9:98277400-98280000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
5	chr9:98277400-98280200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:98277600-98279200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:98277600-98279400	Active TSS	Brain Angular Gyrus	brain
8	chr9:98277600-98279600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:98277600-98279600	Active TSS	Sigmoid Colon	Sigmoid Colon
10	chr9:98277600-98279800	Active TSS	Ovary	ovary
11	chr9:98277600-98280200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr9:98277800-98279000	Flanking Active TSS	Right Ventricle	heart
13	chr9:98277800-98279200	Flanking Bivalent TSS/Enh	Thymus	Thymus
14	chr9:98277800-98279400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:98277800-98279400	Active TSS	HSMM	muscle
16	chr9:98277800-98279400	Active TSS	NHLF	lung
17	chr9:98277800-98279600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr9:98277800-98279600	Active TSS	Gastric	stomach
19	chr9:98277800-98279800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:98277800-98279800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr9:98277800-98279800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr9:98277800-98279800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr9:98277800-98280200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr9:98277800-98280200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr9:98277800-98280200	Active TSS	Brain Cingulate Gyrus	brain
26	chr9:98277800-98280200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:98278000-98279000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:98278000-98279200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:98278000-98279400	Bivalent/Poised TSS	Fetal Stomach	stomach
30	chr9:98278000-98279400	Active TSS	Right Atrium	heart
31	chr9:98278000-98279400	Active TSS	HSMMtube	muscle
32	chr9:98278000-98279600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:98278000-98279600	Active TSS	Fetal Lung	lung
34	chr9:98278000-98279600	Bivalent/Poised TSS	HepG2	liver
35	chr9:98278000-98279600	Active TSS	NHDF-Ad	bronchial
36	chr9:98278000-98279800	Flanking Active TSS	Liver	Liver
37	chr9:98278000-98280000	Active TSS	Brain Anterior Caudate	brain
38	chr9:98278000-98280200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr9:98278000-98280200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr9:98278000-98280200	Active TSS	Brain Substantia Nigra	brain
41	chr9:98278000-98280200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr9:98278200-98279000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
43	chr9:98278200-98279000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr9:98278200-98279200	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr9:98278200-98279200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr9:98278200-98279400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:98278200-98279400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:98278200-98279400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:98278200-98279400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
50	chr9:98278200-98279400	Active TSS	Colon Smooth Muscle	Colon

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