Variant report

Variant	rs9257280
Chromosome Location	chr6:28833507-28833508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:101)
CpG islands
(count:61)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:101 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr6:28833290-28833767	HepG2	liver:	n/a	n/a
2	TAF1	chr6:28833465-28833740	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr6:28833491-28833881	H1-hESC	embryonic stem cell:	n/a	n/a
4	CBX3	chr6:28833095-28834041	K562	blood:	n/a	n/a
5	TCF7L2	chr6:28833010-28833791	HEK293	kidney:	n/a	n/a
6	NFYB	chr6:28833219-28834388	GM12878	blood:	n/a	chr6:28833721-28833736
7	EP300	chr6:28833380-28833876	HepG2	liver:	n/a	n/a
8	SP1	chr6:28833400-28834311	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr6:28833275-28833820	A549	lung:	n/a	n/a
10	GTF2B	chr6:28833502-28833793	K562	blood:	n/a	n/a
11	POLR2A	chr6:28833220-28833781	HepG2	liver:	n/a	n/a
12	ELF1	chr6:28833438-28833765	HepG2	liver:	n/a	n/a
13	NFYB	chr6:28833295-28834269	K562	blood:	n/a	chr6:28833721-28833736
14	POLR2A	chr6:28832767-28833855	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr6:28833404-28833858	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr6:28833505-28833841	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:28833266-28833759	U87	brain:	n/a	n/a
18	POLR2A	chr6:28833399-28833831	H1-neurons	neurons:	n/a	n/a
19	TCF7L2	chr6:28833265-28833821	PANC-1	pancreas:	n/a	n/a
20	MAX	chr6:28833394-28833847	H1-hESC	embryonic stem cell:	n/a	n/a
21	SP1	chr6:28833253-28834578	A549	lung:	n/a	n/a
22	RCOR1	chr6:28833501-28833701	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:28833291-28834002	H1-hESC	embryonic stem cell:	n/a	n/a
24	KAP1	chr6:28833353-28833956	U2OS	brain:	n/a	n/a
25	POLR2A	chr6:28833440-28833799	K562	blood:	n/a	n/a
26	POLR2A	chr6:28833064-28833876	PANC-1	pancreas:	n/a	n/a
27	SP1	chr6:28833389-28834362	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:28833122-28833793	HepG2	liver:	n/a	n/a
29	MAFF	chr6:28833366-28834173	HepG2	liver:	n/a	n/a
30	GTF2F1	chr6:28833475-28833815	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZBTB33	chr6:28833167-28833833	A549	lung:	n/a	n/a
32	POLR2A	chr6:28833439-28833765	HepG2	liver:	n/a	n/a
33	POLR2A	chr6:28833101-28833825	K562	blood:	n/a	n/a
34	EP300	chr6:28833389-28833991	A549	lung:	n/a	n/a
35	NFYA	chr6:28833232-28834278	K562	blood:	n/a	chr6:28833763-28833781 chr6:28833715-28833733
36	CHD2	chr6:28833490-28833702	HepG2	liver:	n/a	n/a
37	SP1	chr6:28833383-28834147	K562	blood:	n/a	n/a
38	ELK4	chr6:28832836-28833683	HEK293	kidney:	n/a	n/a
39	ZMIZ1	chr6:28833507-28833751	K562	blood:	n/a	n/a
40	SP4	chr6:28833449-28833870	H1-hESC	embryonic stem cell:	n/a	n/a
41	NFIC	chr6:28833257-28833979	HepG2	liver:	n/a	n/a
42	HEY1	chr6:28833123-28833874	HepG2	liver:	n/a	n/a
43	HEY1	chr6:28833212-28833718	K562	blood:	n/a	n/a
44	E2F6	chr6:28833266-28833882	H1-hESC	embryonic stem cell:	n/a	n/a
45	NFIC	chr6:28833234-28833870	HepG2	liver:	n/a	n/a
46	MAX	chr6:28833227-28833820	A549	lung:	n/a	n/a
47	POLR2A	chr6:28833435-28833832	NB4	blood:	n/a	n/a
48	POLR2A	chr6:28833035-28833984	HepG2	liver:	n/a	n/a
49	POLR2A	chr6:28832988-28834982	H1-hESC	embryonic stem cell:	n/a	n/a
50	SP1	chr6:28833499-28834275	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28833480-28833530	HMEC	breast:	n/a
2	chr6:28833480-28833530	PANC-1	pancreas:	n/a
3	chr6:28833480-28833530	NHBE	bronchial:	n/a
4	chr6:28833480-28833530	PrEC	prostate:	n/a
5	chr6:28833480-28833530	GM19239	blood:	n/a
6	chr6:28833480-28833530	HRE	kidney:	n/a
7	chr6:28833480-28833530	AG04449	skin:	fetal
8	chr6:28833480-28833530	HNPCEpiC	eye:	n/a
9	chr6:28833480-28833530	RPTEC	kidney:	n/a
10	chr6:28833480-28833530	ECC-1	luminal epithelium:	n/a
11	chr6:28833480-28833530	BE2_C	brain:	n/a
12	chr6:28833480-28833530	Hepatocyte	liver:	n/a
13	chr6:28833480-28833530	SK-N-SH_RA	brain:	n/a
14	chr6:28833480-28833530	HRPEpiC	eye:	n/a
15	chr6:28833480-28833530	Hela-S3	cervix:	n/a
16	chr6:28833480-28833530	AG09319	gingival:	n/a
17	chr6:28833480-28833530	ProgFib	skin:	n/a
18	chr6:28833480-28833530	HCPEpiC	choroid plexus:	n/a
19	chr6:28833480-28833530	HepG2	liver:	n/a
20	chr6:28833480-28833530	AoSMC	blood vessel:	n/a
21	chr6:28833480-28833530	HCF	heart:	n/a
22	chr6:28833480-28833530	SK-N-SH	brain:	n/a
23	chr6:28833480-28833530	GM06990	blood:	n/a
24	chr6:28833480-28833530	Jurkat	blood:	n/a
25	chr6:28833480-28833530	ovcar-3	ovarian:	n/a
26	chr6:28833480-28833530	SAEC	small airway:	n/a
27	chr6:28833480-28833530	HUVEC	blood vessel:	n/a
28	chr6:28833480-28833530	HAEpiC	amniotic membrane:	n/a
29	chr6:28833480-28833530	H1-hESC	embryonic stem cell:	embryo
30	chr6:28833480-28833530	NT2-D1	testis:	n/a
31	chr6:28833480-28833530	HRCEpiC	kidney:	n/a
32	chr6:28833480-28833530	Caco-2	colon:	n/a
33	chr6:28833480-28833530	K562	blood:	n/a
34	chr6:28833480-28833530	NB4	blood:	n/a
35	chr6:28833480-28833530	HEK293	kidney:	embryo
36	chr6:28833480-28833530	AG04450	lung:	fetal
37	chr6:28833480-28833530	HEEpiC	esophagus:	n/a
38	chr6:28833480-28833530	HIPEpiC	eye:	n/a
39	chr6:28833480-28833530	AG10803	skin:	n/a
40	chr6:28833480-28833530	U87	brain:	n/a
41	chr6:28833480-28833530	SK-N-MC	brain:	n/a
42	chr6:28833480-28833530	GM12878	blood:	n/a
43	chr6:28833480-28833530	HL-60	blood:	n/a
44	chr6:28833480-28833530	PFSK-1	brain:	n/a
45	chr6:28833480-28833530	AG09309	skin:	n/a
46	chr6:28833480-28833530	T-47D	breast:	n/a
47	chr6:28833480-28833530	HCM	heart:	n/a
48	chr6:28833480-28833530	CMK	blood:	n/a
49	chr6:28833480-28833530	IMR90	lung:	fetal
50	chr6:28833480-28833530	MCF10A-Er-Src	breast:	n/a

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28803282..28808663-chr6:28829877..28836776,13	K562	blood:
2	chr6:26156500..26158004-chr6:28832615..28834649,2	K562	blood:
3	chr6:28833014..28834989-chr6:28890241..28892787,3	K562	blood:
4	chr6:28832887..28834550-chr6:28979904..28981561,2	K562	blood:
5	chr6:28802885..28808466-chr6:28831550..28836351,8	MCF-7	breast:
6	chr6:28833478..28838269-chr6:28843234..28846516,6	MCF-7	breast:
7	chr6:28833109..28835315-chr6:29719168..29721447,2	K562	blood:
8	chr6:28832613..28834387-chr6:28980061..28982005,2	K562	blood:
9	chr6:28803282..28808495-chr6:28830531..28834946,8	K562	blood:
10	chr6:28833493..28835780-chr6:28880062..28881962,2	MCF-7	breast:
11	chr6:28828478..28839935-chr6:28855092..28866386,31	K562	blood:
12	chr6:28830882..28836292-chr6:28860588..28866545,10	MCF-7	breast:
13	chr6:28833354..28837219-chr6:28837839..28842041,5	MCF-7	breast:
14	chr6:28831130..28836886-chr6:28890033..28892870,9	MCF-7	breast:
15	chr6:28833368..28835844-chr6:28972691..28974962,2	MCF-7	breast:
16	chr6:28831640..28835125-chr6:28890004..28893108,3	MCF-7	breast:
17	chr6:28833368..28834989-chr6:28890241..28892472,3	K562	blood:
18	chr6:28831550..28833211-chr6:28833226..28834745,2	MCF-7	breast:
19	chr6:28823126..28835109-chr6:28859268..28867076,23	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225595	TF binding region
ENSG00000225595	CpG island
ENSG00000204713	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000272236	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10484543	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1061625	0.81[ASN][1000 genomes]
rs172326	0.88[ASN][1000 genomes]
rs1794588	0.82[ASN][1000 genomes]
rs184094	0.89[ASN][1000 genomes]
rs2013652	0.81[ASN][1000 genomes]
rs209127	0.83[ASN][1000 genomes]
rs209140	0.87[ASN][1000 genomes]
rs209147	0.89[ASN][1000 genomes]
rs209151	0.90[ASN][1000 genomes]
rs209165	0.91[ASN][1000 genomes]
rs209172	0.88[ASN][1000 genomes]
rs209177	0.90[ASN][1000 genomes]
rs209180	0.85[ASN][1000 genomes]
rs2148007	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269553	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28381661	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28381663	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28381666	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28400868	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28400869	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28743260	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2894066	0.81[ASN][1000 genomes]
rs3132377	0.81[ASN][1000 genomes]
rs3135314	0.83[ASN][1000 genomes]
rs413972	0.88[ASN][1000 genomes]
rs422331	0.89[ASN][1000 genomes]
rs429369	0.89[ASN][1000 genomes]
rs4484511	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6909419	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs743847	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7750338	0.89[ASN][1000 genomes]
rs7763940	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7769221	0.89[ASN][1000 genomes]
rs7776376	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257269	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9257270	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9257274	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9257281	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9257328	0.89[ASN][1000 genomes]
rs929042	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9348814	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9368576	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378149	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9393932	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9393933	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404976	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
4	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
5	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28830600-28834800	Active TSS	A549	lung
2	chr6:28831000-28834800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:28831000-28835000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28832400-28834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:28832600-28833600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:28832600-28833600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:28832600-28833600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:28832600-28833600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:28832600-28833800	Weak transcription	Brain Angular Gyrus	brain
10	chr6:28832600-28833800	Weak transcription	Fetal Kidney	kidney
11	chr6:28832600-28834000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:28832600-28834000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:28832600-28834000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:28832600-28834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:28832600-28834000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:28832600-28834000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:28832600-28834000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
18	chr6:28832600-28834000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:28832600-28834000	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:28832600-28834000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:28832600-28834000	Weak transcription	Brain Substantia Nigra	brain
22	chr6:28832600-28834000	Weak transcription	Colonic Mucosa	Colon
23	chr6:28832600-28834000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:28832600-28834000	Weak transcription	Pancreas	Pancrea
25	chr6:28832600-28834000	Weak transcription	Right Atrium	heart
26	chr6:28832600-28834000	Weak transcription	HSMMtube	muscle
27	chr6:28832600-28834000	Weak transcription	Osteobl	bone
28	chr6:28832600-28834200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:28832600-28834200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:28832600-28834200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:28832600-28834200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:28832600-28834200	Weak transcription	Aorta	Aorta
33	chr6:28832600-28834200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:28832600-28834200	Weak transcription	Gastric	stomach
35	chr6:28832600-28834200	Weak transcription	Left Ventricle	heart
36	chr6:28832600-28834200	Weak transcription	Lung	lung
37	chr6:28832600-28834200	Weak transcription	Ovary	ovary
38	chr6:28832600-28834200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr6:28832600-28834200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:28832600-28834200	Weak transcription	Spleen	Spleen
41	chr6:28832600-28834200	Weak transcription	NH-A	brain
42	chr6:28832600-28834200	Weak transcription	NHDF-Ad	bronchial
43	chr6:28832600-28835200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr6:28832800-28833600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:28832800-28833600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:28832800-28833600	Weak transcription	Fetal Lung	lung
47	chr6:28832800-28833600	Weak transcription	Thymus	Thymus
48	chr6:28832800-28833600	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:28832800-28833800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:28832800-28833800	Weak transcription	Rectal Mucosa Donor 29	rectum

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