Variant report

Variant	rs1831561
Chromosome Location	chr9:12884932-12884933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:152)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:152 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:12884880-12885030	AG09309	skin:	n/a	n/a
2	CTCF	chr9:12884900-12885050	HepG2	liver:	n/a	n/a
3	CTCF	chr9:12884900-12885050	AoAF	blood vessel:	n/a	n/a
4	FOS	chr9:12884680-12885223	MCF10A-Er-Src	breast:	n/a	chr9:12885188-12885198
5	CTCF	chr9:12884800-12884950	HVMF	connective:	n/a	n/a
6	CTCF	chr9:12884880-12885030	HA-sp	spinal cord:	n/a	n/a
7	CTCF	chr9:12884901-12885031	GM10248	blood:	n/a	n/a
8	RAD21	chr9:12884806-12885078	GM12878	blood:	n/a	n/a
9	MYC	chr9:12884753-12885085	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr9:12884851-12885009	NHEK	skin:	n/a	n/a
11	CTCF	chr9:12884900-12885050	HMF	breast:	n/a	n/a
12	JUND	chr9:12884677-12885205	Hela-S3	cervix:	n/a	chr9:12885188-12885198
13	POLR2A	chr9:12884843-12884975	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr9:12884880-12885030	AG10803	skin:	n/a	n/a
15	CTCF	chr9:12884825-12885103	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr9:12884880-12885030	HRPEpiC	eye:	n/a	n/a
17	RAD21	chr9:12884651-12885333	IMR90	lung:	n/a	n/a
18	CTCF	chr9:12884920-12885070	HEEpiC	esophagus:	n/a	n/a
19	CTCF	chr9:12884920-12885070	A549	lung:	n/a	n/a
20	RAD21	chr9:12884737-12885150	A549	lung:	n/a	n/a
21	CTCF	chr9:12884880-12885030	HCM	heart:	n/a	n/a
22	STAT3	chr9:12884858-12885111	MCF10A-Er-Src	breast:	n/a	chr9:12884887-12884898
23	CTCF	chr9:12884860-12885010	BE2_C	brain:	n/a	n/a
24	SMC3	chr9:12884594-12885489	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr9:12884860-12885010	HCPEpiC	choroid plexus:	n/a	n/a
26	CTCF	chr9:12884867-12885042	ProgFib	skin:	n/a	n/a
27	MAFK	chr9:12884694-12885179	IMR90	lung:	n/a	n/a
28	RAD21	chr9:12884699-12885251	SK-N-SH_RA	brain:	n/a	n/a
29	CTCF	chr9:12884852-12885083	ECC-1	luminal epithelium:	n/a	n/a
30	CTCF	chr9:12884920-12885070	WI-38	lung:	n/a	n/a
31	CTCF	chr9:12884880-12885030	HVMF	connective:	n/a	n/a
32	CTCF	chr9:12884840-12884990	GM12869	blood:	n/a	n/a
33	RAD21	chr9:12884615-12885337	A549	lung:	n/a	n/a
34	CEBPB	chr9:12884711-12885012	IMR90	lung:	n/a	n/a
35	CTCF	chr9:12884824-12885094	K562	blood:	n/a	n/a
36	CTCF	chr9:12884826-12885112	HUVEC	blood vessel:	n/a	n/a
37	CTCF	chr9:12884840-12884990	SK-N-SH_RA	brain:	n/a	n/a
38	CTCF	chr9:12884820-12884970	HCM	heart:	n/a	n/a
39	RAD21	chr9:12884625-12885277	MCF-7	breast:	n/a	n/a
40	FOS	chr9:12884680-12885107	MCF10A-Er-Src	breast:	n/a	n/a
41	MYC	chr9:12884695-12885088	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr9:12884800-12884950	HFF	foreskin:	n/a	n/a
43	STAT3	chr9:12884720-12885100	MCF10A-Er-Src	breast:	n/a	chr9:12884887-12884898
44	CTCF	chr9:12884900-12885050	HCFaa	heart:	n/a	n/a
45	CTCF	chr9:12884860-12885010	Caco-2	colon:	n/a	n/a
46	E2F4	chr9:12884733-12885105	MCF10A-Er-Src	breast:	n/a	n/a
47	CTCF	chr9:12884867-12885068	Spleen_OC	spleen:	n/a	n/a
48	SMC3	chr9:12884648-12885324	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr9:12884871-12885072	Lung_OC	lung:	n/a	n/a
50	CTCF	chr9:12884840-12884990	GM12864	blood:	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: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12344174	0.87[EUR][1000 genomes]
rs13284880	0.93[EUR][1000 genomes]
rs13286083	0.87[EUR][1000 genomes]
rs13295684	0.93[EUR][1000 genomes]
rs13297021	0.93[EUR][1000 genomes]
rs13299801	0.93[EUR][1000 genomes]
rs13300480	0.81[EUR][1000 genomes]
rs13301620	0.81[EUR][1000 genomes]
rs1412308	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16929764	0.93[EUR][1000 genomes]
rs16929768	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16929788	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34040994	0.93[EUR][1000 genomes]
rs34086294	0.87[EUR][1000 genomes]
rs34297034	0.93[EUR][1000 genomes]
rs34660175	0.93[EUR][1000 genomes]
rs35253144	0.88[EUR][1000 genomes]
rs35313919	0.87[EUR][1000 genomes]
rs35685701	0.93[EUR][1000 genomes]
rs35696782	0.93[EUR][1000 genomes]
rs35858006	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36050768	0.87[EUR][1000 genomes]
rs36080084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36196009	0.87[EUR][1000 genomes]
rs71507337	0.87[EUR][1000 genomes]
rs71507342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs978929	0.83[AFR][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:26 , 50 per page) page: 1

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

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