Variant report

Variant	rs540714952
Chromosome Location	chr6:28186412-28186413
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	MAZ	chr6:28186301-28187051	GM12878	blood:	n/a	chr6:28186753-28186763
2	EBF1	chr6:28186291-28186611	GM12878	blood:	n/a	n/a
3	CTCF	chr6:28186400-28186550	WERI-Rb-1	eye:	n/a	n/a
4	POLR2A	chr6:28186322-28186882	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:28186359-28187032	NB4	blood:	n/a	n/a
6	HCFC1	chr6:28186293-28186960	K562	blood:	n/a	n/a
7	CTCF	chr6:28186306-28186881	GM12878	blood:	n/a	chr6:28186586-28186599
8	NFIC	chr6:28186238-28186974	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:28186289-28187012	K562	blood:	n/a	n/a
10	TCF7L2	chr6:28186311-28186545	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr6:28186350-28186972	A549	lung:	n/a	n/a
12	POLR2A	chr6:28186351-28186535	H1-hESC	embryonic stem cell:	n/a	n/a
13	ETS1	chr6:28186382-28186862	K562	blood:	n/a	chr6:28186762-28186773 chr6:28186756-28186767 chr6:28186471-28186480 chr6:28186592-28186605 chr6:28186753-28186764 chr6:28186471-28186480
14	POLR2A	chr6:28186280-28187021	K562	blood:	n/a	n/a
15	ZMIZ1	chr6:28186349-28187014	K562	blood:	n/a	n/a
16	POLR2A	chr6:28186338-28187036	Gliobla	brain:	n/a	n/a
17	ZNF143	chr6:28186343-28186960	GM12878	blood:	n/a	chr6:28186687-28186705
18	GABPA	chr6:28186351-28186937	HepG2	liver:	n/a	chr6:28186758-28186767 chr6:28186710-28186719
19	ELF1	chr6:28186115-28187009	MCF-7	breast:	n/a	n/a
20	CTCF	chr6:28186400-28186550	HCFaa	heart:	n/a	n/a
21	TAF1	chr6:28186212-28187027	K562	blood:	n/a	n/a
22	MAFK	chr6:28186369-28186492	K562	blood:	n/a	n/a
23	MAX	chr6:28186264-28187069	MCF-7	breast:	n/a	chr6:28186753-28186763
24	POLR2A	chr6:28186297-28186960	K562	blood:	n/a	n/a
25	GABPA	chr6:28186315-28187094	HL-60	blood:	n/a	chr6:28186758-28186767 chr6:28186710-28186719
26	RUNX3	chr6:28186264-28187017	GM12878	blood:	n/a	n/a
27	CTCF	chr6:28186280-28186430	BJ	skin:	n/a	n/a
28	MAX	chr6:28186371-28187059	H1-hESC	embryonic stem cell:	n/a	chr6:28186753-28186763
29	TCF12	chr6:28186397-28186617	GM12878	blood:	n/a	n/a
30	TAF1	chr6:28186328-28186593	HepG2	liver:	n/a	n/a
31	GABPA	chr6:28186341-28187126	SK-N-SH	brain:	n/a	chr6:28186758-28186767 chr6:28186710-28186719
32	MYC	chr6:28186397-28186481	MCF-7	breast:	n/a	n/a
33	POLR2A	chr6:28186367-28186570	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:28186019-28187004	K562	blood:	n/a	n/a
35	MAZ	chr6:28186348-28186937	Hela-S3	cervix:	n/a	chr6:28186753-28186763
36	ELK1	chr6:28186320-28186926	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:28186325-28187019	GM15510	blood:	n/a	n/a
38	CTCF	chr6:28186404-28186567	GM12891	blood:	n/a	n/a
39	POLR2A	chr6:28186372-28187008	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr6:28186401-28186562	GM19240	blood:	n/a	n/a
41	TAF1	chr6:28186323-28186553	GM12892	blood:	n/a	n/a
42	POLR2A	chr6:28186130-28187136	HepG2	liver:	n/a	n/a
43	POLR2A	chr6:28186308-28187024	HepG2	liver:	n/a	n/a
44	POLR2A	chr6:28186255-28187042	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr6:28186275-28187002	PFSK-1	brain:	n/a	n/a
46	MAX	chr6:28186334-28187074	SK-N-SH	brain:	n/a	chr6:28186753-28186763
47	TAF1	chr6:28186209-28186715	H1-hESC	embryonic stem cell:	n/a	n/a
48	TCF12	chr6:28186328-28187134	A549	lung:	n/a	chr6:28186860-28186867 chr6:28186625-28186635
49	POLR2A	chr6:28185956-28187137	Hela-S3	cervix:	n/a	n/a
50	HEY1	chr6:28186219-28187085	HepG2	liver:	n/a	chr6:28186714-28186729 chr6:28186869-28186884

No.	Distal block	Cell Line	Cell type
1	chr6:28184931..28189194-chr6:28190077..28194573,12	MCF-7	breast:
2	chr6:28184339..28187958-chr6:28190844..28194750,7	MCF-7	breast:
3	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
4	chr6:28108272..28111912-chr6:28184259..28187979,3	MCF-7	breast:
5	chr6:28143030..28145517-chr6:28186267..28188999,2	K562	blood:
6	chr6:28185564..28187470-chr6:28218621..28220714,2	MCF-7	breast:
7	chr6:27805809..27807448-chr6:28184413..28187037,2	MCF-7	breast:
8	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
9	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
10	chr6:28100317..28107200-chr6:28184436..28191088,8	MCF-7	breast:
11	chr6:28104139..28106070-chr6:28185714..28187223,2	MCF-7	breast:
12	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
13	chr6:27775362..27779371-chr6:28186093..28189957,4	K562	blood:
14	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
15	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
16	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:

Variant related genes	Relation type
TOB2P1	TF binding region
ENSG00000184348	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000216901	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000187626	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	nsv527115	chr6:28185726-28186554	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28184600-28186600	Enhancers	Spleen	Spleen
2	chr6:28185600-28186600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:28185600-28187000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:28185600-28187400	Active TSS	Stomach Smooth Muscle	stomach
5	chr6:28185800-28186600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:28185800-28187000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr6:28185800-28187200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:28186000-28186600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:28186000-28186600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
10	chr6:28186000-28186600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr6:28186000-28186600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
12	chr6:28186000-28186600	Flanking Active TSS	Placenta	Placenta
13	chr6:28186000-28186600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr6:28186000-28187000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr6:28186000-28187000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:28186000-28187000	Active TSS	HSMM	muscle
17	chr6:28186000-28187000	Active TSS	HSMMtube	muscle
18	chr6:28186000-28187200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:28186000-28187200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:28186000-28187200	Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:28186000-28187200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
22	chr6:28186000-28187200	Active TSS	NHLF	lung
23	chr6:28186000-28187200	Active TSS	Osteobl	bone
24	chr6:28186200-28186600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:28186200-28186600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
26	chr6:28186200-28186600	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr6:28186200-28186600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:28186200-28186600	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
29	chr6:28186200-28186600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr6:28186200-28186600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:28186200-28186600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:28186200-28186600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:28186200-28186600	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:28186200-28186600	Flanking Active TSS	Liver	Liver
35	chr6:28186200-28186600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
36	chr6:28186200-28186600	Flanking Bivalent TSS/Enh	Ovary	ovary
37	chr6:28186200-28186600	Flanking Active TSS	Pancreas	Pancrea
38	chr6:28186200-28186600	Flanking Active TSS	HMEC	breast
39	chr6:28186200-28186600	Flanking Active TSS	NH-A	brain
40	chr6:28186200-28186800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:28186200-28186800	Active TSS	Fetal Intestine Large	intestine
42	chr6:28186200-28187000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr6:28186200-28187000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:28186200-28187000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:28186200-28187000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
46	chr6:28186200-28187000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
47	chr6:28186200-28187000	Active TSS	Colonic Mucosa	Colon
48	chr6:28186200-28187000	Active TSS	Esophagus	oesophagus
49	chr6:28186200-28187000	Active TSS	Fetal Kidney	kidney
50	chr6:28186200-28187000	Active TSS	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links