Variant report

Variant	rs2780988
Chromosome Location	chr9:86212113-86212114
allele	C/T
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	chr9:86211857-86212189	H1-hESC	embryonic stem cell:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
2	CTCF	chr9:86211857-86212157	SK-N-SH_RA	brain:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
3	CTCF	chr9:86211888-86212147	GM10266	blood:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
4	SMC3	chr9:86211820-86212200	Hela-S3	cervix:	n/a	n/a
5	ZNF143	chr9:86212041-86212170	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr9:86211797-86212217	H1-hESC	embryonic stem cell:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
7	CTCF	chr9:86211907-86212144	MCF-7	breast:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
8	CTCF	chr9:86211823-86212137	A549	lung:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
9	JUND	chr9:86211928-86212141	K562	blood:	n/a	n/a
10	RAD21	chr9:86211777-86212162	H1-hESC	embryonic stem cell:	n/a	chr9:86212001-86212020
11	RAD21	chr9:86211732-86212229	H1-hESC	embryonic stem cell:	n/a	chr9:86212001-86212020
12	RAD21	chr9:86211794-86212205	Hela-S3	cervix:	n/a	chr9:86212001-86212020
13	RAD21	chr9:86211532-86212400	SK-N-SH	brain:	n/a	chr9:86212001-86212020
14	ZNF143	chr9:86211790-86212172	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr9:86211863-86212154	IMR90	lung:	n/a	chr9:86212001-86212020
16	CTCF	chr9:86211887-86212146	GM19239	blood:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
17	CTCF	chr9:86211907-86212128	Lung_OC	lung:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
18	CTCF	chr9:86211904-86212123	LNCaP	prostate:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
19	RAD21	chr9:86211722-86212170	ECC-1	luminal epithelium:	n/a	chr9:86212001-86212020
20	CTCF	chr9:86211258-86212533	A549	lung:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212471-86212480 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
21	CTCF	chr9:86211864-86212204	Gliobla	brain:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
22	CTCF	chr9:86211602-86212336	HCT-116	colon:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
23	CTCF	chr9:86211896-86212149	Fibrobl	skin:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
24	RAD21	chr9:86211858-86212168	K562	blood:	n/a	chr9:86212001-86212020
25	CTCF	chr9:86211900-86212133	LNCaP	prostate:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
26	ZNF143	chr9:86211856-86212179	K562	blood:	n/a	n/a
27	CTCF	chr9:86211915-86212139	ECC-1	luminal epithelium:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
28	CTCF	chr9:86211886-86212156	Medullo	brain:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
29	EBF1	chr9:86211891-86212180	GM12878	blood:	n/a	chr9:86212071-86212081 chr9:86212070-86212081
30	ZNF143	chr9:86211851-86212181	GM12878	blood:	n/a	n/a
31	RAD21	chr9:86211729-86212207	SK-N-SH_RA	brain:	n/a	chr9:86212001-86212020
32	CTCF	chr9:86211895-86212163	ProgFib	skin:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
33	CTCF	chr9:86211860-86212287	MCF-7	breast:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
34	CTCF	chr9:86211860-86212218	GM19238	blood:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
35	EBF1	chr9:86211960-86212195	GM12878	blood:	n/a	chr9:86212071-86212081 chr9:86212070-86212081
36	RAD21	chr9:86211584-86212260	HCT-116	colon:	n/a	chr9:86212001-86212020
37	CTCF	chr9:86211944-86212133	GM20000	blood:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
38	CTCF	chr9:86211902-86212141	Kidney_OC	kidney:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
39	CTCF	chr9:86211914-86212142	GM13977	blood:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
40	RAD21	chr9:86211743-86212216	HepG2	liver:	n/a	chr9:86212001-86212020
41	RAD21	chr9:86211863-86212187	HepG2	liver:	n/a	chr9:86212001-86212020
42	EBF1	chr9:86211856-86212211	GM12878	blood:	n/a	chr9:86212071-86212081 chr9:86212070-86212081
43	CTCF	chr9:86211943-86212152	GM13976	blood:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
44	ZKSCAN1	chr9:86211985-86212185	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr9:86211874-86212169	A549	lung:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
46	CTCF	chr9:86211809-86212223	K562	blood:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
47	CTCF	chr9:86211821-86212152	K562	blood:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
48	CTCF	chr9:86211867-86212167	GM19240	blood:	n/a	chr9:86211887-86211900 chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
49	CTCF	chr9:86211888-86212153	NHEK	skin:	n/a	chr9:86211998-86212019 chr9:86212003-86212021 chr9:86212004-86212020 chr9:86212005-86212018
50	RAD21	chr9:86211803-86212161	GM12878	blood:	n/a	chr9:86212001-86212020

No.	Distal block	Cell Line	Cell type
1	chr9:86153641..86154250-chr9:86211840..86212460,2	MCF-7	breast:
2	chr9:86153344..86154235-chr9:86211597..86212500,2	MCF-7	breast:
3	chr9:85834621..85835782-chr9:86211520..86212262,3	MCF-7	breast:

Variant related genes	Relation type
RNU4-15P	TF binding region
ENSG00000172159	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10114717	1.00[ASN][1000 genomes]
rs10116424	1.00[ASN][1000 genomes]
rs10121045	1.00[ASN][1000 genomes]
rs10121882	1.00[ASN][1000 genomes]
rs10122131	1.00[ASN][1000 genomes]
rs10122134	1.00[ASN][1000 genomes]
rs10123002	1.00[ASN][1000 genomes]
rs10124333	1.00[ASN][1000 genomes]
rs10125987	1.00[ASN][1000 genomes]
rs10481738	1.00[ASN][1000 genomes]
rs11140184	1.00[ASN][1000 genomes]
rs11140193	1.00[ASN][1000 genomes]
rs11140196	1.00[ASN][1000 genomes]
rs11140201	1.00[ASN][1000 genomes]
rs11140213	1.00[ASN][1000 genomes]
rs12335711	1.00[ASN][1000 genomes]
rs12340935	1.00[ASN][1000 genomes]
rs12342901	1.00[ASN][1000 genomes]
rs12343837	1.00[ASN][1000 genomes]
rs12344615	1.00[ASN][1000 genomes]
rs12345514	1.00[ASN][1000 genomes]
rs12351677	1.00[ASN][1000 genomes]
rs13284999	1.00[ASN][1000 genomes]
rs13289229	1.00[ASN][1000 genomes]
rs13291631	1.00[ASN][1000 genomes]
rs13292088	1.00[ASN][1000 genomes]
rs13294533	1.00[ASN][1000 genomes]
rs13301956	1.00[ASN][1000 genomes]
rs2780983	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780985	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs2780987	1.00[CEU][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780989	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2811898	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555298	1.00[ASN][1000 genomes]
rs3447	1.00[ASN][1000 genomes]
rs34778713	1.00[ASN][1000 genomes]
rs34891935	1.00[ASN][1000 genomes]
rs35378833	1.00[ASN][1000 genomes]
rs35535452	1.00[ASN][1000 genomes]
rs4364707	1.00[ASN][1000 genomes]
rs7045761	1.00[ASN][1000 genomes]
rs9314722	1.00[ASN][1000 genomes]
rs944947	1.00[ASN][1000 genomes]
rs9987871	1.00[ASN][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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1038884	chr9:86089963-86215800	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86188000-86215200	Weak transcription	Primary T cells from cord blood	blood
2	chr9:86198800-86217800	Weak transcription	Aorta	Aorta

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