Variant report

Variant	rs543442189
Chromosome Location	chr6:56707636-56707637
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	CEBPB	chr6:56707559-56707652	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:56707616-56709245	GM19193	blood:	n/a	n/a
3	SIN3A	chr6:56707523-56709292	H1-hESC	embryonic stem cell:	n/a	chr6:56708586-56708599 chr6:56708333-56708344
4	RAD21	chr6:56707393-56708245	IMR90	lung:	n/a	chr6:56708102-56708112
5	STAT5A	chr6:56707503-56708287	GM12878	blood:	n/a	chr6:56707600-56707614
6	RUNX3	chr6:56707614-56708544	GM12878	blood:	n/a	n/a
7	MXI1	chr6:56707183-56709485	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:56707345-56709348	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr6:56707514-56709185	ProgFib	skin:	n/a	n/a
10	POLR2A	chr6:56707320-56709243	H1-neurons	neurons:	n/a	n/a
11	MTA3	chr6:56707527-56708000	GM12878	blood:	n/a	n/a
12	EBF1	chr6:56707449-56708152	GM12878	blood:	n/a	n/a
13	CHD1	chr6:56707490-56708200	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr6:56707313-56709296	H1-neurons	neurons:	n/a	n/a
15	ZEB1	chr6:56707473-56708525	GM12878	blood:	n/a	n/a
16	MXI1	chr6:56707426-56709479	IMR90	lung:	n/a	n/a
17	POLR2A	chr6:56707365-56709352	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr6:56707603-56708700	Gliobla	brain:	n/a	n/a
19	STAT3	chr6:56707549-56707728	MCF10A-Er-Src	breast:	n/a	chr6:56707601-56707612 chr6:56707600-56707614
20	MTA3	chr6:56707261-56708281	GM12878	blood:	n/a	n/a
21	CHD1	chr6:56704985-56709414	IMR90	lung:	n/a	n/a
22	REST	chr6:56707146-56709449	H1-neurons	neurons:	n/a	chr6:56708116-56708129 chr6:56708326-56708344 chr6:56708603-56708616 chr6:56708593-56708603 chr6:56707162-56707171
23	CHD1	chr6:56707606-56708307	GM12878	blood:	n/a	n/a
24	ZNF263	chr6:56707490-56708523	HEK293-T-REx	kidney:	n/a	n/a
25	RUNX3	chr6:56707632-56708531	GM12878	blood:	n/a	n/a
26	RAD21	chr6:56707317-56709429	SK-N-SH	brain:	n/a	chr6:56709008-56709021 chr6:56708102-56708112
27	POLR2A	chr6:56707624-56709237	GM12892	blood:	n/a	n/a
28	MAX	chr6:56707570-56708308	MCF-7	breast:	n/a	n/a
29	CTCF	chr6:56707400-56709488	SK-N-SH	brain:	n/a	n/a
30	MYC	chr6:56707543-56708107	MCF10A-Er-Src	breast:	n/a	n/a
31	SMC3	chr6:56707534-56707671	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr6:56707515-56709356	H1-hESC	embryonic stem cell:	n/a	n/a
33	PML	chr6:56707400-56708339	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:56707508-56709261	GM12878	blood:	n/a	n/a
35	KAP1	chr6:56707457-56708175	HEK293	kidney:	n/a	n/a
36	TCF7L2	chr6:56707624-56708218	PANC-1	pancreas:	n/a	n/a
37	SMC3	chr6:56707332-56709475	SK-N-SH	brain:	n/a	n/a
38	MAZ	chr6:56707236-56709454	IMR90	lung:	n/a	chr6:56708634-56708644 chr6:56708654-56708663
39	ELF1	chr6:56707527-56709232	GM12878	blood:	n/a	chr6:56708382-56708391 chr6:56708170-56708182 chr6:56708374-56708386 chr6:56708613-56708625
40	MAX	chr6:56707566-56708608	MCF-7	breast:	n/a	n/a
41	SIN3AK20	chr6:56707456-56709274	PANC-1	pancreas:	n/a	n/a
42	STAT3	chr6:56707530-56707703	MCF10A-Er-Src	breast:	n/a	chr6:56707601-56707612 chr6:56707600-56707614
43	STAT3	chr6:56707452-56707767	MCF10A-Er-Src	breast:	n/a	chr6:56707601-56707612 chr6:56707600-56707614
44	POLR2A	chr6:56707575-56709203	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56707257..56710686-chr6:56712186..56717279,8	MCF-7	breast:
2	chr6:56704167..56710132-chr6:56712428..56720773,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231441	TF binding region
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3338248	chr6:56707418-56709966	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3350484	chr6:56707493-56709741	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr6:56704000-56709400	Active TSS	Right Atrium	heart
2	chr6:56704200-56709200	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr6:56704600-56709200	Active TSS	HSMMtube	muscle
4	chr6:56704800-56709400	Active TSS	HSMM	muscle
5	chr6:56705000-56709400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:56705200-56709400	Active TSS	Right Ventricle	heart
7	chr6:56705400-56708000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:56705400-56708000	Flanking Active TSS	HUVEC	blood vessel
9	chr6:56705400-56709200	Active TSS	Brain Cingulate Gyrus	brain
10	chr6:56705400-56709200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:56705600-56708200	Active TSS	Fetal Heart	heart
12	chr6:56705600-56709200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:56705600-56709200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:56705600-56709200	Active TSS	Aorta	Aorta
15	chr6:56705600-56709200	Active TSS	Left Ventricle	heart
16	chr6:56705600-56709200	Active TSS	Stomach Smooth Muscle	stomach
17	chr6:56705600-56709200	Active TSS	NHLF	lung
18	chr6:56705600-56709400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:56705800-56709200	Active TSS	A549	lung
20	chr6:56705800-56709400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:56705800-56709400	Active TSS	Brain Anterior Caudate	brain
22	chr6:56706000-56709000	Active TSS	Fetal Brain Female	brain
23	chr6:56706000-56709200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:56706000-56709200	Active TSS	Ovary	ovary
25	chr6:56706200-56707800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
26	chr6:56706200-56709200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:56706200-56709200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr6:56706200-56709200	Active TSS	GM12878-XiMat	blood
29	chr6:56706200-56709400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr6:56706400-56707800	Active TSS	Brain Germinal Matrix	brain
31	chr6:56706400-56709200	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr6:56706400-56709200	Active TSS	Brain Angular Gyrus	brain
33	chr6:56706400-56709400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr6:56706600-56709200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr6:56706800-56708200	Active TSS	Fetal Brain Male	brain
36	chr6:56706800-56709000	Active TSS	NHDF-Ad	bronchial
37	chr6:56706800-56709200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:56706800-56709200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr6:56706800-56709200	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:56706800-56709400	Active TSS	Brain Substantia Nigra	brain
41	chr6:56707000-56708800	Active TSS	NH-A	brain
42	chr6:56707000-56709200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:56707000-56709200	Active TSS	Brain Hippocampus Middle	brain
44	chr6:56707200-56707800	Flanking Active TSS	HMEC	breast
45	chr6:56707200-56708200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:56707200-56708800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:56707200-56709200	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr6:56707200-56709200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:56707200-56709200	Active TSS	Colon Smooth Muscle	Colon
50	chr6:56707200-56709200	Active TSS	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links