Variant report

Variant	rs568460988
Chromosome Location	chr6:4778178-4778179
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	RELA	chr6:4777462-4778900	GM12878	blood:	n/a	n/a
2	RELA	chr6:4777389-4778895	GM18951	blood:	n/a	n/a
3	ATF2	chr6:4778161-4778898	GM12878	blood:	n/a	n/a
4	STAT5A	chr6:4778064-4778852	GM12878	blood:	n/a	chr6:4778684-4778695
5	POLR2A	chr6:4777394-4778648	GM12891	blood:	n/a	n/a
6	CHD2	chr6:4777462-4778287	GM12878	blood:	n/a	n/a
7	CREB1	chr6:4778167-4778918	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:4777261-4778617	GM12891	blood:	n/a	n/a
9	POLR2A	chr6:4777385-4778548	GM12878	blood:	n/a	n/a
10	NFATC1	chr6:4778028-4779019	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:4777962-4778574	GM12892	blood:	n/a	n/a
12	FOXM1	chr6:4778155-4778867	GM12878	blood:	n/a	n/a
13	ATF2	chr6:4778124-4778824	GM12878	blood:	n/a	n/a
14	CBX3	chr6:4778104-4778750	K562	blood:	n/a	n/a
15	SETDB1	chr6:4778111-4778964	U2OS	brain:	n/a	n/a
16	NFIC	chr6:4778165-4778686	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:4778157-4778509	GM12891	blood:	n/a	n/a
18	TBL1XR1	chr6:4778142-4778972	GM12878	blood:	n/a	n/a
19	BHLHE40	chr6:4777336-4778808	GM12878	blood:	n/a	n/a
20	KAP1	chr6:4777817-4779068	K562	blood:	n/a	n/a
21	KAP1	chr6:4777767-4778872	HEK293	kidney:	n/a	n/a
22	MTA3	chr6:4778058-4778837	GM12878	blood:	n/a	n/a
23	PML	chr6:4778009-4778800	GM12878	blood:	n/a	n/a
24	EBF1	chr6:4778134-4778757	GM12878	blood:	n/a	n/a
25	TBP	chr6:4777392-4779043	GM12878	blood:	n/a	n/a
26	CEBPB	chr6:4777403-4778870	GM12878	blood:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
27	MTA3	chr6:4778155-4778738	GM12878	blood:	n/a	n/a
28	RELA	chr6:4777413-4778869	GM19193	blood:	n/a	n/a
29	POLR2A	chr6:4777148-4778610	GM12892	blood:	n/a	n/a
30	ZNF143	chr6:4778029-4778970	GM12878	blood:	n/a	n/a
31	NFIC	chr6:4777359-4779165	GM12878	blood:	n/a	n/a
32	MXI1	chr6:4775628-4778903	SK-N-SH	brain:	n/a	chr6:4776030-4776039
33	POLR2A	chr6:4775177-4778562	GM18505	blood:	n/a	n/a
34	RUNX3	chr6:4777284-4778919	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:4778157-4778489	GM12891	blood:	n/a	n/a
36	POLR2A	chr6:4776093-4778983	GM12878	blood:	n/a	n/a
37	KAP1	chr6:4778005-4778800	U2OS	brain:	n/a	n/a
38	MAZ	chr6:4774846-4778791	IMR90	lung:	n/a	chr6:4775819-4775828 chr6:4776302-4776311 chr6:4777256-4777266
39	RUNX3	chr6:4777891-4778606	GM12878	blood:	n/a	n/a
40	WRNIP1	chr6:4777483-4778203	GM12878	blood:	n/a	n/a
41	SMC3	chr6:4777461-4778244	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:4775838-4778573	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4775417..4779410-chr6:4834974..4837006,3	MCF-7	breast:
2	chr6:4773447..4776687-chr6:4777915..4782551,4	MCF-7	breast:
3	chr6:4776139..4778956-chr6:5002447..5004557,2	K562	blood:
4	chr6:4488845..4492110-chr6:4777740..4781440,3	MCF-7	breast:
5	chr6:4775727..4780301-chr6:4925378..4930668,5	K562	blood:
6	chr6:4778081..4781516-chr6:4787216..4791667,5	MCF-7	breast:
7	chr6:4777710..4780092-chr6:4801744..4804702,2	K562	blood:
8	chr6:4776830..4778493-chr6:4928400..4930186,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236336	TF binding region
ENSG00000236336	Chromatin interaction
ENSG00000124787	Chromatin interaction
ENSG00000153046	Chromatin interaction
ENSG00000260239	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv3358796	chr6:4775353-4778326	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3445880	chr6:4775978-4778526	Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4773200-4778200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:4775000-4778400	Active TSS	Brain Cingulate Gyrus	brain
3	chr6:4775000-4778400	Active TSS	A549	lung
4	chr6:4775200-4778400	Active TSS	Aorta	Aorta
5	chr6:4775600-4778200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:4775600-4778200	Active TSS	Left Ventricle	heart
7	chr6:4775600-4778400	Active TSS	Right Ventricle	heart
8	chr6:4775600-4778600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:4775800-4778200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:4775800-4778200	Active TSS	Colonic Mucosa	Colon
11	chr6:4775800-4778200	Active TSS	Duodenum Mucosa	Duodenum
12	chr6:4775800-4778200	Active TSS	Fetal Muscle Trunk	muscle
13	chr6:4775800-4778400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:4775800-4778400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr6:4775800-4778400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:4775800-4778400	Active TSS	NH-A	brain
17	chr6:4775800-4778800	Active TSS	GM12878-XiMat	blood
18	chr6:4775800-4778800	Active TSS	NHLF	lung
19	chr6:4776200-4778400	Active TSS	Right Atrium	heart
20	chr6:4776400-4778200	Active TSS	Brain Germinal Matrix	brain
21	chr6:4776400-4778400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:4777200-4778400	Active TSS	Placenta	Placenta
23	chr6:4777400-4778200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr6:4777400-4778200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:4777400-4778200	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr6:4777400-4778200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr6:4777400-4778200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr6:4777400-4778400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr6:4777400-4778400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr6:4777400-4778400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:4777400-4778400	Flanking Active TSS	Liver	Liver
32	chr6:4777400-4778400	Flanking Active TSS	Fetal Brain Male	brain
33	chr6:4777400-4778600	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr6:4777400-4778600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:4777400-4778600	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr6:4777600-4778200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
37	chr6:4777600-4778200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr6:4777600-4778200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr6:4777600-4778200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:4777600-4778200	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr6:4777600-4778400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr6:4777600-4778400	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr6:4777600-4778400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:4777600-4778400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:4777600-4778400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:4777600-4778400	Flanking Active TSS	Fetal Heart	heart
47	chr6:4777600-4778400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr6:4777600-4778400	Flanking Bivalent TSS/Enh	HepG2	liver
49	chr6:4777600-4778400	Flanking Active TSS	HUVEC	blood vessel
50	chr6:4777600-4778600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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