Variant report

Variant	rs28555298
Chromosome Location	chr9:86320233-86320234
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	CEBPB	chr9:86320041-86320386	IMR90	lung:	n/a	chr9:86320211-86320222
2	CEBPB	chr9:86320025-86320393	Hela-S3	cervix:	n/a	chr9:86320211-86320222
3	ZNF384	chr9:86319759-86320329	K562	blood:	n/a	n/a
4	CEBPB	chr9:86320134-86320307	HepG2	liver:	n/a	chr9:86320211-86320222
5	ZNF384	chr9:86319701-86321305	GM12878	blood:	n/a	n/a
6	CEBPB	chr9:86320030-86320402	HepG2	liver:	n/a	chr9:86320211-86320222
7	POLR2A	chr9:86320226-86320242	HepG2	liver:	n/a	n/a
8	CEBPB	chr9:86320091-86320268	K562	blood:	n/a	chr9:86320211-86320222
9	CEBPB	chr9:86320050-86320399	A549	lung:	n/a	chr9:86320211-86320222
10	MYC	chr9:86320072-86320236	NB4	blood:	n/a	n/a
11	CEBPB	chr9:86320025-86320405	HepG2	liver:	n/a	chr9:86320211-86320222
12	CEBPB	chr9:86319997-86320402	MCF-7	breast:	n/a	chr9:86320211-86320222
13	CEBPB	chr9:86320026-86320321	H1-hESC	embryonic stem cell:	n/a	chr9:86320211-86320222
14	CEBPB	chr9:86319951-86320401	K562	blood:	n/a	chr9:86320211-86320222
15	RUNX3	chr9:86320231-86320712	GM12878	blood:	n/a	n/a
16	CEBPB	chr9:86320016-86320308	HepG2	liver:	n/a	chr9:86320211-86320222
17	CEBPB	chr9:86319946-86320379	K562	blood:	n/a	chr9:86320211-86320222
18	POLR2A	chr9:86320128-86320480	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:85832727..85836639-chr9:86319596..86323973,3	MCF-7	breast:
2	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
3	chr9:86310182..86311687-chr9:86319047..86320880,2	K562	blood:

Variant related genes	Relation type
ENSG00000254473	TF binding region
ENSG00000229109	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000178966	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10114717	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115073	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10116424	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121045	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121882	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123002	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124333	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125987	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481738	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140184	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140193	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140196	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140201	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12335711	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340935	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342901	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343837	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351677	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284999	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289229	1.00[ASN][1000 genomes]
rs13291631	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13292088	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13294533	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301956	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780983	1.00[ASN][1000 genomes]
rs2780987	1.00[ASN][1000 genomes]
rs2780988	1.00[ASN][1000 genomes]
rs2780989	1.00[ASN][1000 genomes]
rs2811898	1.00[ASN][1000 genomes]
rs3447	1.00[ASN][1000 genomes]
rs34778713	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34891935	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35378833	1.00[ASN][1000 genomes]
rs35535452	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364707	1.00[ASN][1000 genomes]
rs7045761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314722	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987871	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
2	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
4	chr9:86297600-86321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:86298000-86320400	Weak transcription	Fetal Intestine Large	intestine
6	chr9:86298600-86320400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:86298800-86320800	Weak transcription	Fetal Thymus	thymus
8	chr9:86300400-86320400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:86300600-86320400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:86301000-86320800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr9:86304400-86320800	Weak transcription	Brain Anterior Caudate	brain
12	chr9:86307600-86320400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr9:86310400-86320600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:86311200-86320800	Weak transcription	Fetal Lung	lung
15	chr9:86311800-86321000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:86312800-86320800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr9:86313200-86320800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr9:86313600-86321000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr9:86314400-86320800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr9:86314600-86321400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:86314600-86321400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:86314600-86321400	Weak transcription	Gastric	stomach
23	chr9:86314600-86321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:86315000-86320400	Weak transcription	Fetal Heart	heart
25	chr9:86315000-86320600	Weak transcription	Stomach Mucosa	stomach
26	chr9:86315200-86321400	Weak transcription	Aorta	Aorta
27	chr9:86315600-86320400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:86315800-86320800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:86315800-86320800	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:86316000-86320400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:86316000-86320600	Weak transcription	Brain Substantia Nigra	brain
32	chr9:86316000-86321400	Weak transcription	Pancreas	Pancrea
33	chr9:86316000-86321800	Weak transcription	Lung	lung
34	chr9:86316600-86320400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:86316800-86320400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr9:86317000-86320400	Weak transcription	Adipose Nuclei	Adipose
37	chr9:86317000-86320600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr9:86317000-86320800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:86317000-86321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:86317200-86320400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:86317200-86320600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:86317200-86320600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:86317200-86320600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:86317200-86320600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:86317200-86320600	Weak transcription	Brain Angular Gyrus	brain
46	chr9:86317200-86320600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr9:86317200-86320600	Weak transcription	NH-A	brain
48	chr9:86317200-86320600	Weak transcription	Osteobl	bone
49	chr9:86317200-86320800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr9:86317200-86320800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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