Variant report

Variant	rs559978106
Chromosome Location	chr6:4134920-4134921
allele	G/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	SIN3A	chr6:4134395-4135873	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr6:4134635-4135031	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr6:4134214-4135809	PBDE	blood:	n/a	n/a
4	BHLHE40	chr6:4134279-4134930	K562	blood:	n/a	n/a
5	BHLHE40	chr6:4134431-4135779	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:4134212-4135928	HepG2	liver:	n/a	n/a
7	CEBPB	chr6:4134655-4134981	HepG2	liver:	n/a	chr6:4134853-4134864 chr6:4134854-4134865
8	MYC	chr6:4134276-4136820	K562	blood:	n/a	chr6:4136289-4136298
9	RFX5	chr6:4134307-4135793	Hela-S3	cervix:	n/a	chr6:4135632-4135640
10	POLR2A	chr6:4134238-4135044	HepG2	liver:	n/a	n/a
11	MXI1	chr6:4134305-4135808	GM12878	blood:	n/a	n/a
12	TBP	chr6:4134719-4135927	HepG2	liver:	n/a	n/a
13	TBL1XR1	chr6:4134263-4135720	K562	blood:	n/a	n/a
14	TEAD4	chr6:4134014-4135039	K562	blood:	n/a	n/a
15	CEBPB	chr6:4134675-4135037	HepG2	liver:	n/a	chr6:4134853-4134864 chr6:4134854-4134865
16	MYBL2	chr6:4134059-4134979	HepG2	liver:	n/a	n/a
17	JUN	chr6:4134895-4135250	K562	blood:	n/a	n/a
18	POLR2A	chr6:4134256-4136602	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr6:4134619-4134978	Hela-S3	cervix:	n/a	chr6:4134853-4134864 chr6:4134854-4134865
20	RUNX3	chr6:4134913-4135807	GM12878	blood:	n/a	n/a
21	CBX3	chr6:4134169-4134920	K562	blood:	n/a	chr6:4134467-4134478
22	IRF1	chr6:4133973-4135818	K562	blood:	n/a	chr6:4135177-4135190 chr6:4134990-4135001 chr6:4135178-4135192 chr6:4134988-4135001 chr6:4135178-4135190 chr6:4135178-4135191 chr6:4135178-4135191 chr6:4135179-4135193 chr6:4135178-4135189 chr6:4134988-4135001 chr6:4135177-4135197 chr6:4135178-4135191 chr6:4135178-4135191 chr6:4134936-4134952
23	HNF4A	chr6:4134658-4135020	HepG2	liver:	n/a	chr6:4134876-4134890 chr6:4134881-4134889 chr6:4134875-4134890
24	NFIC	chr6:4134261-4134925	HepG2	liver:	n/a	n/a
25	TBP	chr6:4134224-4135796	Hela-S3	cervix:	n/a	n/a
26	UBTF	chr6:4134026-4135847	K562	blood:	n/a	n/a
27	HNF4G	chr6:4134118-4134962	HepG2	liver:	n/a	chr6:4134876-4134890 chr6:4134292-4134310 chr6:4134881-4134889 chr6:4134295-4134307 chr6:4134295-4134307 chr6:4134875-4134890
28	BRCA1	chr6:4134788-4135758	Hela-S3	cervix:	n/a	n/a
29	EP300	chr6:4134748-4135420	GM12878	blood:	n/a	chr6:4134991-4135005 chr6:4134851-4134865
30	MYC	chr6:4134097-4136687	K562	blood:	n/a	chr6:4136289-4136298
31	CHD1	chr6:4134762-4135251	H1-hESC	embryonic stem cell:	n/a	n/a
32	HNF4A	chr6:4134604-4135019	HepG2	liver:	n/a	chr6:4134876-4134890 chr6:4134881-4134889 chr6:4134875-4134890
33	CHD1	chr6:4134536-4135763	GM12878	blood:	n/a	n/a
34	CEBPB	chr6:4134751-4134960	HepG2	liver:	n/a	chr6:4134853-4134864 chr6:4134854-4134865
35	MBD4	chr6:4134524-4135842	HepG2	liver:	n/a	n/a
36	ARID3A	chr6:4134680-4135751	HepG2	liver:	n/a	chr6:4135064-4135080
37	MXI1	chr6:4133783-4136945	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4056059..4057941-chr6:4133460..4135296,2	K562	blood:
2	chr6:4134858..4135600-chr6:74230356..74231112,2	Hela-S3	cervix:
3	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
4	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:

Variant related genes	Relation type
ENSG00000254821	TF binding region
ECI2	TF binding region
ENSG00000234817	TF binding region
ENSG00000156508	Chromatin interaction
ENSG00000230648	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000272248	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv3413228	chr6:4134778-4137526	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv3369872	chr6:4134903-4137401	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4133800-4135000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:4133800-4135000	Flanking Active TSS	HUVEC	blood vessel
3	chr6:4133800-4136800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr6:4133800-4136800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:4134000-4135000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr6:4134000-4135000	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr6:4134000-4135000	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr6:4134000-4135000	Flanking Active TSS	Dnd41	blood
9	chr6:4134000-4135000	Flanking Active TSS	NH-A	brain
10	chr6:4134000-4135200	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr6:4134000-4135600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:4134000-4136800	Active TSS	Ovary	ovary
13	chr6:4134000-4136800	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr6:4134200-4135000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:4134200-4135000	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:4134200-4135000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr6:4134200-4135000	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr6:4134200-4135000	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr6:4134200-4135000	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr6:4134200-4135000	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr6:4134200-4135000	Flanking Active TSS	HMEC	breast
22	chr6:4134200-4135200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:4134200-4135200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:4134200-4135200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr6:4134200-4135400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:4134200-4135800	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr6:4134200-4136800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:4134200-4136800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:4134200-4137000	Active TSS	Aorta	Aorta
30	chr6:4134400-4135000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:4134400-4135000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:4134400-4135000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:4134400-4135000	Flanking Active TSS	Fetal Lung	lung
34	chr6:4134400-4135000	Enhancers	Lung	lung
35	chr6:4134400-4135400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr6:4134400-4136600	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr6:4134400-4136600	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr6:4134400-4136600	Active TSS	Fetal Brain Female	brain
39	chr6:4134400-4136600	Active TSS	Hela-S3	cervix
40	chr6:4134400-4136800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:4134400-4137000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:4134600-4135000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:4134600-4135000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr6:4134600-4135000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr6:4134600-4135000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr6:4134600-4135200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:4134600-4135200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr6:4134600-4135200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:4134600-4135200	Weak transcription	Spleen	Spleen
50	chr6:4134600-4135400	Active TSS	Right Atrium	heart

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