Variant report

Variant	rs543395986
Chromosome Location	chr21:45580447-45580448
allele	-/GCCCC
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	NFIC	chr21:45578498-45580543	GM12878	blood:	n/a	chr21:45579544-45579572
2	POLR2A	chr21:45578629-45581133	GM18526	blood:	n/a	n/a
3	POLR2A	chr21:45572928-45581556	GM12878	blood:	n/a	n/a
4	POLR2A	chr21:45578463-45581426	GM12892	blood:	n/a	n/a
5	POLR2A	chr21:45578519-45581150	GM12892	blood:	n/a	n/a
6	NR3C1	chr21:45579961-45580500	A549	lung:	n/a	n/a
7	MYC	chr21:45580078-45580450	MCF-7	breast:	n/a	n/a
8	STAT5A	chr21:45580202-45580926	GM12878	blood:	n/a	chr21:45580754-45580766
9	CHD2	chr21:45578588-45581136	GM12878	blood:	n/a	n/a
10	MTA3	chr21:45579576-45581093	GM12878	blood:	n/a	n/a
11	POLR2A	chr21:45578547-45581170	HL-60	blood:	n/a	n/a
12	POLR2A	chr21:45576498-45581335	GM12891	blood:	n/a	n/a
13	POLR2A	chr21:45578763-45581143	GM12891	blood:	n/a	n/a
14	EBF1	chr21:45579140-45581393	GM12878	blood:	n/a	chr21:45581234-45581247 chr21:45581235-45581245 chr21:45581236-45581245 chr21:45580762-45580772
15	POLR2A	chr21:45578806-45581049	GM15510	blood:	n/a	n/a
16	MTA3	chr21:45578504-45581427	GM12878	blood:	n/a	n/a
17	POLR2A	chr21:45578462-45581396	GM12892	blood:	n/a	n/a
18	POLR2A	chr21:45578579-45581303	HL-60	blood:	n/a	n/a
19	POLR2A	chr21:45578637-45581350	GM12878	blood:	n/a	n/a
20	POLR2A	chr21:45578640-45581161	GM12878	blood:	n/a	n/a
21	POLR2A	chr21:45578680-45581072	GM12878	blood:	n/a	n/a
22	POLR2A	chr21:45578594-45581129	GM18951	blood:	n/a	n/a
23	POLR2A	chr21:45578510-45581471	GM12878	blood:	n/a	n/a
24	POLR2A	chr21:45578570-45581070	GM12892	blood:	n/a	n/a
25	POLR2A	chr21:45578683-45581388	GM19193	blood:	n/a	n/a
26	POLR2A	chr21:45578673-45581415	GM12891	blood:	n/a	n/a
27	POLR2A	chr21:45578761-45581407	GM12891	blood:	n/a	n/a
28	POLR2A	chr21:45578782-45581098	GM10847	blood:	n/a	n/a
29	POLR2A	chr21:45578812-45581060	GM18505	blood:	n/a	n/a
30	ELF1	chr21:45579133-45581040	GM12878	blood:	n/a	n/a
31	POLR2A	chr21:45578654-45581250	GM19099	blood:	n/a	n/a
32	POLR2A	chr21:45578597-45581337	GM12878	blood:	n/a	n/a
33	POU2F2	chr21:45578744-45581431	GM12878	blood:	n/a	chr21:45579641-45579653 chr21:45579502-45579514 chr21:45579534-45579546
34	POLR2A	chr21:45579422-45581288	GM12892	blood:	n/a	n/a
35	POU2F2	chr21:45579487-45580679	GM12891	blood:	n/a	chr21:45579641-45579653 chr21:45579502-45579514 chr21:45579534-45579546
36	POU2F2	chr21:45580399-45580963	GM12878	blood:	n/a	n/a
37	POLR2A	chr21:45576448-45581388	GM12878	blood:	n/a	n/a
38	POLR2A	chr21:45578670-45581079	GM12878	blood:	n/a	n/a
39	POU2F2	chr21:45579366-45580574	GM12891	blood:	n/a	chr21:45579641-45579653 chr21:45579502-45579514 chr21:45579534-45579546
40	PAX5	chr21:45579431-45580497	GM12878	blood:	n/a	n/a
41	POLR2A	chr21:45579515-45581045	GM12891	blood:	n/a	n/a
42	MAX	chr21:45578697-45581235	GM12878	blood:	n/a	n/a
43	NR3C1	chr21:45579741-45580526	A549	lung:	n/a	n/a
44	POLR2A	chr21:45580430-45580485	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45551834..45580791-chr21:45711953..45732193,97	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ICOSLG-6	chr21:45578913-45580684	XLOC_014110

Variant related genes	Relation type
ENSG00000225331	TF binding region
ENSG00000141959	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv913890	chr21:45482950-45603746	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription 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	32 gene(s)	inside rSNPs	diseases
7	nsv459294	chr21:45499171-45595060	Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv587722	chr21:45499171-45595060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv913891	chr21:45508561-45588518	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv913892	chr21:45508561-45595060	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv913893	chr21:45508561-45603746	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv913895	chr21:45528919-45595060	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv913896	chr21:45528919-45603746	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS 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	52 gene(s)	inside rSNPs	diseases
17	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription 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	65 gene(s)	inside rSNPs	diseases
18	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
19	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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	74 gene(s)	inside rSNPs	diseases
20	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
21	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv913899	chr21:45577102-45611950	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
24	esv3398689	chr21:45580349-45583097	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45561000-45584400	Weak transcription	Aorta	Aorta
2	chr21:45565400-45580600	Weak transcription	Brain Germinal Matrix	brain
3	chr21:45571000-45582600	Weak transcription	Ovary	ovary
4	chr21:45575400-45583400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:45575400-45586000	Weak transcription	Fetal Lung	lung
6	chr21:45575400-45592000	Weak transcription	Fetal Brain Female	brain
7	chr21:45575600-45584800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr21:45576000-45580600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:45576600-45580600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr21:45576600-45580600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr21:45576600-45581200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr21:45576800-45580600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr21:45577200-45580600	Enhancers	Fetal Muscle Trunk	muscle
14	chr21:45577200-45581000	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr21:45577600-45581400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr21:45578600-45580600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr21:45578800-45581400	Flanking Active TSS	GM12878-XiMat	blood
18	chr21:45579000-45580800	Enhancers	HUVEC	blood vessel
19	chr21:45579000-45581000	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr21:45579000-45581200	Enhancers	Lung	lung
21	chr21:45579200-45580800	Enhancers	Fetal Intestine Small	intestine
22	chr21:45579200-45580800	Enhancers	Stomach Mucosa	stomach
23	chr21:45579200-45581000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr21:45579200-45581200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr21:45579400-45580600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr21:45579400-45580800	Enhancers	Gastric	stomach
27	chr21:45579400-45581000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr21:45579400-45581000	Enhancers	Pancreas	Pancrea
29	chr21:45579400-45581200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr21:45579400-45581400	Enhancers	Esophagus	oesophagus
31	chr21:45579600-45580800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr21:45579600-45580800	Enhancers	Right Ventricle	heart
33	chr21:45579600-45581200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr21:45579800-45580600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr21:45579800-45580600	Enhancers	Brain Angular Gyrus	brain
36	chr21:45579800-45580600	Enhancers	Left Ventricle	heart
37	chr21:45579800-45580600	Weak transcription	Small Intestine	intestine
38	chr21:45579800-45581000	Enhancers	Right Atrium	heart
39	chr21:45579800-45581000	Enhancers	Spleen	Spleen
40	chr21:45579800-45581200	Enhancers	Primary T cells from cord blood	blood
41	chr21:45579800-45581400	Enhancers	Brain Anterior Caudate	brain
42	chr21:45579800-45581600	Enhancers	Placenta	Placenta
43	chr21:45579800-45583000	Enhancers	Fetal Muscle Leg	muscle
44	chr21:45579800-45590400	Weak transcription	Colon Smooth Muscle	Colon
45	chr21:45579800-45590400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr21:45580000-45580600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr21:45580000-45580600	Enhancers	Adipose Nuclei	Adipose
48	chr21:45580000-45591200	Weak transcription	Fetal Heart	heart
49	chr21:45580200-45580600	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr21:45580200-45580800	Flanking Active TSS	Brain Substantia Nigra	brain

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