Variant report

Variant	rs1780152
Chromosome Location	chr9:15142946-15142947
allele	A/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	CTCF	chr9:15142916-15143301	K562	blood:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
2	RAD21	chr9:15142893-15143337	MCF-7	breast:	n/a	chr9:15143099-15143118
3	RAD21	chr9:15142888-15143252	SK-N-SH_RA	brain:	n/a	chr9:15143099-15143118
4	CTCF	chr9:15142720-15143528	SK-N-SH	brain:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
5	SMC3	chr9:15142934-15143284	GM12878	blood:	n/a	chr9:15143103-15143117 chr9:15143110-15143117
6	ZNF143	chr9:15142945-15143296	GM12878	blood:	n/a	n/a
7	GATA2	chr9:15142842-15143271	SH-SY5Y	brain:	n/a	chr9:15143084-15143098 chr9:15143061-15143068
8	CTCF	chr9:15142945-15143270	HUVEC	blood vessel:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
9	RAD21	chr9:15142917-15143256	K562	blood:	n/a	chr9:15143099-15143118
10	CTCF	chr9:15142862-15143276	H1-hESC	embryonic stem cell:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
11	CTCF	chr9:15142923-15143347	MCF-7	breast:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
12	CTCF	chr9:15142910-15143191	A549	lung:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
13	RAD21	chr9:15142939-15143257	A549	lung:	n/a	chr9:15143099-15143118
14	CTCF	chr9:15142882-15143217	K562	blood:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
15	RAD21	chr9:15142860-15143323	H1-hESC	embryonic stem cell:	n/a	chr9:15143099-15143118
16	SMC3	chr9:15142892-15143307	Hela-S3	cervix:	n/a	chr9:15143103-15143117 chr9:15143110-15143117
17	CTCF	chr9:15142939-15143234	SK-N-SH_RA	brain:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
18	GATA2	chr9:15142879-15143237	HUVEC	blood vessel:	n/a	chr9:15143084-15143098 chr9:15143061-15143068
19	USF2	chr9:15142946-15143249	H1-hESC	embryonic stem cell:	n/a	n/a
20	TEAD4	chr9:15142866-15143367	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr9:15142547-15143510	A549	lung:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
22	CTCF	chr9:15142926-15143273	K562	blood:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
23	RAD21	chr9:15142200-15143508	SK-N-SH	brain:	n/a	chr9:15143099-15143118
24	TEAD4	chr9:15142851-15143286	K562	blood:	n/a	n/a
25	SMC3	chr9:15142923-15143305	HepG2	liver:	n/a	chr9:15143103-15143117 chr9:15143110-15143117
26	CTCF	chr9:15142878-15143231	HepG2	liver:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
27	RAD21	chr9:15142771-15143382	HCT-116	colon:	n/a	chr9:15143099-15143118
28	RAD21	chr9:15142875-15143198	HepG2	liver:	n/a	chr9:15143099-15143118
29	BRCA1	chr9:15142912-15143159	H1-hESC	embryonic stem cell:	n/a	n/a
30	GATA3	chr9:15142814-15143215	T-47D	breast:	n/a	chr9:15143061-15143068
31	RAD21	chr9:15142889-15143284	HepG2	liver:	n/a	chr9:15143099-15143118
32	CTCF	chr9:15142861-15143320	IMR90	lung:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
33	SIN3A	chr9:15142887-15143214	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr9:15142942-15143201	T-47D	breast:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
35	CTCF	chr9:15142928-15143271	ECC-1	luminal epithelium:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
36	CTCF	chr9:15142936-15143221	A549	lung:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
37	RAD21	chr9:15142844-15143322	A549	lung:	n/a	chr9:15143099-15143118
38	RAD21	chr9:15142782-15143374	H1-hESC	embryonic stem cell:	n/a	chr9:15143099-15143118
39	RAD21	chr9:15142908-15143172	GM12878	blood:	n/a	chr9:15143099-15143118
40	MYC	chr9:15142812-15143016	H1-hESC	embryonic stem cell:	n/a	n/a
41	SMC3	chr9:15142922-15143278	K562	blood:	n/a	chr9:15143103-15143117 chr9:15143110-15143117
42	TEAD4	chr9:15142853-15143331	HepG2	liver:	n/a	n/a
43	GATA3	chr9:15142798-15143235	T-47D	breast:	n/a	chr9:15143061-15143068
44	GATA3	chr9:15142852-15143429	MCF-7	breast:	n/a	chr9:15143061-15143068
45	RAD21	chr9:15142920-15143340	MCF-7	breast:	n/a	chr9:15143099-15143118
46	CTCF	chr9:15142889-15143176	K562	blood:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
47	RAD21	chr9:15142827-15143253	SK-N-SH_RA	brain:	n/a	chr9:15143099-15143118
48	CTCF	chr9:15142776-15143400	HCT-116	colon:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
49	CTCF	chr9:15142840-15143384	MCF-7	breast:	n/a	chr9:15143102-15143118 chr9:15143096-15143117 chr9:15143101-15143119
50	USF2	chr9:15142869-15143149	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15114564..15116499-chr9:15140559..15143275,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-559P	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1746330	0.90[AFR][1000 genomes]
rs1780161	0.90[AFR][1000 genomes]
rs2186027	1.00[AFR][1000 genomes]
rs2489541	0.94[AFR][1000 genomes]
rs2761092	0.81[AFR][1000 genomes]
rs2761103	0.87[AFR][1000 genomes]
rs2761110	0.94[AFR][1000 genomes]
rs2761111	0.94[AFR][1000 genomes]
rs2761114	0.94[AFR][1000 genomes]
rs2761117	0.84[AFR][1000 genomes]
rs2800569	0.94[AFR][1000 genomes]
rs2800597	0.81[AFR][1000 genomes]
rs2800614	0.90[AFR][1000 genomes]
rs2800616	0.90[AFR][1000 genomes]
rs2800619	0.90[AFR][1000 genomes]
rs2800620	0.90[AFR][1000 genomes]
rs4305996	0.84[AFR][1000 genomes]
rs4741458	0.80[AFR][1000 genomes]
rs6474894	0.80[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831519	chr9:15018160-15209127	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1019567	chr9:15031398-15159409	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15135400-15146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:15135600-15144600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:15135800-15144400	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:15135800-15144800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:15135800-15146000	Weak transcription	Brain Germinal Matrix	brain
6	chr9:15137200-15156000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:15137400-15147000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:15138800-15146600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:15138800-15146800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:15139000-15146600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:15139600-15146600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:15139800-15146200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:15140200-15144600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:15140200-15146600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:15140400-15144600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:15141000-15144600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:15141000-15154400	Weak transcription	Fetal Stomach	stomach
18	chr9:15141800-15143200	Enhancers	Fetal Thymus	thymus
19	chr9:15142400-15143000	Enhancers	Primary T cells from cord blood	blood
20	chr9:15142400-15143000	Enhancers	Thymus	Thymus
21	chr9:15142600-15143000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr9:15142600-15143000	Enhancers	Fetal Lung	lung
23	chr9:15142600-15143200	Enhancers	Dnd41	blood
24	chr9:15142800-15143000	Enhancers	Colon Smooth Muscle	Colon
25	chr9:15142800-15143000	Enhancers	Fetal Kidney	kidney
26	chr9:15142800-15143000	Enhancers	K562	blood
27	chr9:15142800-15143200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr9:15142800-15143200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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