Variant report

Variant	rs558677279
Chromosome Location	chr6:45390215-45390216
allele	-/C
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	chr6:45389403-45390492	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr6:45389303-45390284	HEK293-T-REx	kidney:	n/a	n/a
3	EP300	chr6:45389200-45391505	SK-N-SH	brain:	n/a	n/a
4	MAZ	chr6:45389117-45390768	Hela-S3	cervix:	n/a	chr6:45389137-45389147
5	MAX	chr6:45389245-45390616	A549	lung:	n/a	n/a
6	TCF7L2	chr6:45389467-45390734	HCT-116	colon:	n/a	n/a
7	HMGN3	chr6:45389378-45390828	K562	blood:	n/a	n/a
8	MYC	chr6:45389687-45390780	MCF-7	breast:	n/a	n/a
9	E2F6	chr6:45389325-45390239	K562	blood:	n/a	n/a
10	MAX	chr6:45389313-45391254	NB4	blood:	n/a	n/a
11	RAD21	chr6:45388419-45392074	IMR90	lung:	n/a	chr6:45391794-45391808 chr6:45392039-45392052 chr6:45390904-45390916 chr6:45390740-45390753 chr6:45391581-45391591 chr6:45388466-45388478
12	POLR2A	chr6:45389182-45392710	HL-60	blood:	n/a	n/a
13	POLR2A	chr6:45389134-45390316	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:45389166-45392571	HL-60	blood:	n/a	n/a
15	CHD1	chr6:45388363-45391883	IMR90	lung:	n/a	chr6:45391066-45391076 chr6:45391635-45391645
16	ZBTB7A	chr6:45389772-45390362	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr6:45390156-45390641	H1-neurons	neurons:	n/a	n/a
18	SMC3	chr6:45389042-45390791	Hela-S3	cervix:	n/a	n/a
19	SIN3A	chr6:45389123-45390301	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF143	chr6:45390066-45391433	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr6:45389301-45392277	MCF-7	breast:	n/a	n/a
22	RAD21	chr6:45390193-45392102	H1-hESC	embryonic stem cell:	n/a	chr6:45391794-45391808 chr6:45392039-45392052 chr6:45390904-45390916 chr6:45390740-45390753 chr6:45391581-45391591
23	RAD21	chr6:45389324-45390230	A549	lung:	n/a	n/a
24	CHD2	chr6:45389267-45390419	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr6:45389565-45390231	MCF-7	breast:	n/a	n/a
26	TCF7L2	chr6:45389274-45390267	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr6:45390026-45390543	IMR90	lung:	n/a	n/a
28	MAX	chr6:45389255-45390289	ECC-1	luminal epithelium:	n/a	n/a
29	MAX	chr6:45389364-45390815	MCF-7	breast:	n/a	n/a
30	POLR2A	chr6:45389639-45390223	ProgFib	skin:	n/a	n/a
31	SIN3AK20	chr6:45389659-45390905	PANC-1	pancreas:	n/a	n/a
32	MXI1	chr6:45389223-45392118	IMR90	lung:	n/a	n/a
33	EP300	chr6:45390168-45390459	SK-N-SH_RA	brain:	n/a	n/a
34	EP300	chr6:45390102-45390916	ECC-1	luminal epithelium:	n/a	n/a
35	RAD21	chr6:45389075-45390508	HCT-116	colon:	n/a	n/a
36	RCOR1	chr6:45389314-45390257	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr6:45389830-45390273	U87	brain:	n/a	n/a
38	POLR2A	chr6:45389241-45392606	NB4	blood:	n/a	n/a
39	POLR2A	chr6:45388936-45390689	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr6:45389830-45390267	U87	brain:	n/a	n/a
41	MAZ	chr6:45389116-45390826	K562	blood:	n/a	chr6:45389137-45389147
42	EGR1	chr6:45389781-45390237	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr6:45389484-45390407	U87	brain:	n/a	n/a
44	POLR2A	chr6:45390154-45391276	Gliobla	brain:	n/a	n/a
45	RAD21	chr6:45389238-45390285	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr6:45389150-45390255	Hela-S3	cervix:	n/a	n/a
47	UBTF	chr6:45389247-45390406	K562	blood:	n/a	n/a
48	HDAC2	chr6:45389227-45390501	MCF-7	breast:	n/a	n/a
49	MAZ	chr6:45389048-45392554	IMR90	lung:	n/a	chr6:45391434-45391444 chr6:45389137-45389147
50	CCNT2	chr6:45389391-45390801	K562	blood:	n/a	n/a

Variant related genes	Relation type
RUNX2	TF binding region
ENSG00000271857	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3495915	chr6:45388574-45392472	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3495916	chr6:45388574-45392472	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45387000-45391800	Bivalent Enhancer	Fetal Brain Male	brain
2	chr6:45387000-45392200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:45387200-45390800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
4	chr6:45387400-45391000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:45388200-45390800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
6	chr6:45388200-45391800	Active TSS	Ovary	ovary
7	chr6:45388200-45392000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:45388200-45392000	Active TSS	NHDF-Ad	bronchial
9	chr6:45388200-45392400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:45388400-45393400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:45388600-45390800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:45388600-45390800	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr6:45388600-45390800	Active TSS	Small Intestine	intestine
14	chr6:45388600-45391000	Active TSS	Brain Angular Gyrus	brain
15	chr6:45388600-45391600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:45388600-45391800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr6:45388600-45392000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr6:45388600-45392200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:45388600-45392800	Active TSS	HSMM	muscle
20	chr6:45388600-45393000	Active TSS	NHLF	lung
21	chr6:45388800-45390800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:45388800-45390800	Active TSS	Brain Anterior Caudate	brain
23	chr6:45388800-45391400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:45388800-45391800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:45388800-45391800	Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:45388800-45392000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr6:45388800-45392400	Active TSS	HSMMtube	muscle
28	chr6:45389000-45390400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:45389000-45391200	Active TSS	HMEC	breast
30	chr6:45389000-45391800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:45389000-45392200	Active TSS	Osteobl	bone
32	chr6:45389000-45392400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr6:45389000-45392400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:45389000-45392600	Active TSS	Monocytes-CD14+_RO01746	blood
35	chr6:45389200-45390400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
36	chr6:45389200-45390400	Flanking Active TSS	Liver	Liver
37	chr6:45389200-45390400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
38	chr6:45389200-45390800	Active TSS	Fetal Kidney	kidney
39	chr6:45389200-45391000	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr6:45389200-45391600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:45389200-45391600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
42	chr6:45389200-45391600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr6:45389200-45391800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:45389200-45391800	Active TSS	NH-A	brain
45	chr6:45389200-45392000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr6:45389200-45392000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:45389200-45392000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:45389200-45392000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:45389200-45392000	Active TSS	Brain Substantia Nigra	brain
50	chr6:45389200-45392000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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