Variant report

Variant	rs16923068
Chromosome Location	chr9:12884779-12884780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr9:12884680-12885223	MCF10A-Er-Src	breast:	n/a	chr9:12885188-12885198
2	MYC	chr9:12884753-12885085	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr9:12884677-12885205	Hela-S3	cervix:	n/a	chr9:12885188-12885198
4	RAD21	chr9:12884651-12885333	IMR90	lung:	n/a	n/a
5	RAD21	chr9:12884737-12885150	A549	lung:	n/a	n/a
6	SMC3	chr9:12884594-12885489	SK-N-SH	brain:	n/a	n/a
7	MAFK	chr9:12884694-12885179	IMR90	lung:	n/a	n/a
8	RAD21	chr9:12884699-12885251	SK-N-SH_RA	brain:	n/a	n/a
9	RAD21	chr9:12884615-12885337	A549	lung:	n/a	n/a
10	CEBPB	chr9:12884711-12885012	IMR90	lung:	n/a	n/a
11	RAD21	chr9:12884625-12885277	MCF-7	breast:	n/a	n/a
12	FOS	chr9:12884680-12885107	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr9:12884695-12885088	MCF10A-Er-Src	breast:	n/a	n/a
14	STAT3	chr9:12884720-12885100	MCF10A-Er-Src	breast:	n/a	chr9:12884887-12884898
15	E2F4	chr9:12884733-12885105	MCF10A-Er-Src	breast:	n/a	n/a
16	SMC3	chr9:12884648-12885324	Hela-S3	cervix:	n/a	n/a
17	RAD21	chr9:12884727-12885189	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr9:12884704-12885243	HCT-116	colon:	n/a	n/a
19	CTCF	chr9:12884714-12885143	HepG2	liver:	n/a	n/a
20	CTCF	chr9:12884681-12885208	MCF-7	breast:	n/a	n/a
21	RAD21	chr9:12884658-12885243	HepG2	liver:	n/a	n/a
22	CHD1	chr9:12884646-12885406	IMR90	lung:	n/a	n/a
23	RAD21	chr9:12884719-12885205	ECC-1	luminal epithelium:	n/a	n/a
24	SMC3	chr9:12884673-12885152	HepG2	liver:	n/a	n/a
25	CTCF	chr9:12884686-12885228	A549	lung:	n/a	n/a
26	RAD21	chr9:12884603-12885529	SK-N-SH	brain:	n/a	n/a
27	RFX5	chr9:12884759-12885168	Hela-S3	cervix:	n/a	n/a
28	STAT3	chr9:12884720-12885105	MCF10A-Er-Src	breast:	n/a	chr9:12884887-12884898
29	POLR2A	chr9:12884745-12885324	IMR90	lung:	n/a	n/a
30	STAT3	chr9:12884724-12885105	MCF10A-Er-Src	breast:	n/a	chr9:12884887-12884898
31	CTCF	chr9:12884743-12885228	IMR90	lung:	n/a	n/a
32	CTCF	chr9:12884556-12885391	SK-N-SH	brain:	n/a	n/a
33	CEBPB	chr9:12884687-12885143	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr9:12884703-12885175	A549	lung:	n/a	n/a
35	RAD21	chr9:12884699-12885190	H1-hESC	embryonic stem cell:	n/a	n/a
36	RAD21	chr9:12884700-12885240	ECC-1	luminal epithelium:	n/a	n/a
37	NR2F2	chr9:12884698-12885186	MCF-7	breast:	n/a	n/a
38	CTCF	chr9:12884754-12885168	GM12878	blood:	n/a	n/a
39	RAD21	chr9:12884727-12885202	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr9:12884760-12884910	A549	lung:	n/a	n/a
41	CTCF	chr9:12884606-12885284	HCT-116	colon:	n/a	n/a
42	CTCF	chr9:12884764-12885155	MCF-7	breast:	n/a	n/a
43	RAD21	chr9:12884767-12885149	H1-hESC	embryonic stem cell:	n/a	n/a
44	FOS	chr9:12884678-12885086	MCF10A-Er-Src	breast:	n/a	n/a
45	RAD21	chr9:12884618-12885331	HCT-116	colon:	n/a	n/a
46	FOS	chr9:12884683-12885063	MCF10A-Er-Src	breast:	n/a	n/a
47	RAD21	chr9:12884635-12885291	A549	lung:	n/a	n/a
48	RAD21	chr9:12884617-12885430	MCF-7	breast:	n/a	n/a
49	RAD21	chr9:12884754-12885181	HepG2	liver:	n/a	n/a
50	RAD21	chr9:12884632-12885404	HCT-116	colon:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:12883524..12885050-chr9:12887759..12890204,2	MCF-7	breast:
2	chr9:12776937..12779598-chr9:12883479..12885184,2	MCF-7	breast:
3	chr9:12774954..12777056-chr9:12883374..12886318,3	MCF-7	breast:
4	chr9:12774893..12776821-chr9:12883465..12885141,2	MCF-7	breast:
5	chr9:12719062..12719862-chr9:12884578..12885277,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000222658	TF binding region
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1328908	1.00[AMR][1000 genomes]
rs1332067	1.00[AMR][1000 genomes]
rs1332073	1.00[AMR][1000 genomes]
rs1410775	1.00[AMR][1000 genomes]
rs1412302	1.00[AMR][1000 genomes]
rs16929699	1.00[AMR][1000 genomes]
rs16929728	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16929797	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2382389	1.00[AMR][1000 genomes]
rs35856256	1.00[AMR][1000 genomes]
rs4281192	1.00[AMR][1000 genomes]
rs6474746	1.00[AMR][1000 genomes]
rs7852730	1.00[EUR][1000 genomes]
rs7853482	1.00[EUR][1000 genomes]
rs7864857	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv613615	chr9:12830070-12947238	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12875200-12884800	Weak transcription	HMEC	breast
2	chr9:12879000-12884800	Weak transcription	Liver	Liver
3	chr9:12879000-12884800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr9:12881000-12884800	Weak transcription	Fetal Kidney	kidney
5	chr9:12881000-12899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:12881200-12884800	Weak transcription	Fetal Intestine Small	intestine
7	chr9:12881200-12891200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:12882600-12884800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:12882600-12885400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:12882800-12884800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:12882800-12884800	Weak transcription	Adipose Nuclei	Adipose
12	chr9:12882800-12884800	Weak transcription	Fetal Lung	lung
13	chr9:12882800-12884800	Weak transcription	NH-A	brain
14	chr9:12883000-12884800	Weak transcription	A549	lung
15	chr9:12883600-12884800	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:12883600-12884800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:12883800-12884800	Weak transcription	NHDF-Ad	bronchial
18	chr9:12883800-12885000	Weak transcription	HSMMtube	muscle
19	chr9:12884000-12885000	Weak transcription	Osteobl	bone
20	chr9:12884400-12885200	Enhancers	Hela-S3	cervix
21	chr9:12884600-12885000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr9:12884600-12885000	Enhancers	Stomach Mucosa	stomach
23	chr9:12884600-12885200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:12884600-12885400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:12884600-12885400	Enhancers	Muscle Satellite Cultured Cells	--

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