Variant report

Variant	rs559302574
Chromosome Location	chr21:40176808-40176809
allele	A/G
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	MXI1	chr21:40176328-40180482	SK-N-SH	brain:	n/a	chr21:40176631-40176646 chr21:40176633-40176648
2	POLR2A	chr21:40175826-40184443	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr21:40176800-40178471	NB4	blood:	n/a	chr21:40177454-40177463 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
4	RAD21	chr21:40176494-40178046	ECC-1	luminal epithelium:	n/a	chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178030-40178044
5	TCF7L2	chr21:40176617-40177947	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr21:40176660-40176810	HUVEC	blood vessel:	n/a	n/a
7	USF2	chr21:40176599-40177107	Hela-S3	cervix:	n/a	chr21:40176808-40176819
8	EP300	chr21:40176364-40180305	SK-N-SH	brain:	n/a	chr21:40179345-40179359 chr21:40177988-40177997 chr21:40178219-40178228 chr21:40179343-40179357 chr21:40178259-40178275 chr21:40179344-40179358 chr21:40178028-40178044 chr21:40179342-40179356 chr21:40178328-40178344 chr21:40178322-40178331
9	TCF12	chr21:40176681-40178155	A549	lung:	n/a	n/a
10	RAD21	chr21:40176426-40178698	MCF-7	breast:	n/a	chr21:40178543-40178556 chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178101-40178114 chr21:40178124-40178136 chr21:40178030-40178044
11	E2F6	chr21:40176650-40178180	K562	blood:	n/a	chr21:40177209-40177226 chr21:40178104-40178114 chr21:40177212-40177223
12	HDAC2	chr21:40176800-40177224	K562	blood:	n/a	n/a
13	SMC3	chr21:40176607-40178615	Hela-S3	cervix:	n/a	chr21:40177519-40177533 chr21:40177325-40177332 chr21:40178167-40178177 chr21:40177094-40177108 chr21:40178332-40178342 chr21:40177523-40177533
14	MYC	chr21:40176696-40178074	K562	blood:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
15	SMARCC1	chr21:40176513-40177935	Hela-S3	cervix:	n/a	chr21:40176655-40176664
16	FOS	chr21:40176288-40177165	MCF10A-Er-Src	breast:	n/a	chr21:40176540-40176547 chr21:40176651-40176662 chr21:40176536-40176545 chr21:40176654-40176665 chr21:40176655-40176663 chr21:40176309-40176317 chr21:40176535-40176546 chr21:40176653-40176664
17	SMC3	chr21:40175857-40180616	SK-N-SH	brain:	n/a	chr21:40177519-40177533 chr21:40177325-40177332 chr21:40178167-40178177 chr21:40177094-40177108 chr21:40178332-40178342 chr21:40177523-40177533
18	MAZ	chr21:40175795-40179353	IMR90	lung:	n/a	chr21:40176308-40176317 chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40176537-40176546 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
19	RAD21	chr21:40176793-40178075	HCT-116	colon:	n/a	chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178030-40178044
20	ZNF263	chr21:40176729-40178117	K562	blood:	n/a	chr21:40177796-40177817
21	POLR2A	chr21:40176494-40176962	HepG2	liver:	n/a	n/a
22	KAP1	chr21:40176666-40177759	HEK293	kidney:	n/a	n/a
23	RAD21	chr21:40176569-40179264	IMR90	lung:	n/a	chr21:40178543-40178556 chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178101-40178114 chr21:40178124-40178136 chr21:40178030-40178044
24	MAX	chr21:40176586-40178175	A549	lung:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
25	CTCF	chr21:40176319-40179110	SK-N-SH	brain:	n/a	chr21:40177982-40177995 chr21:40177095-40177108 chr21:40177092-40177110 chr21:40177520-40177533
26	POLR2A	chr21:40175924-40187316	MCF10A-Er-Src	breast:	n/a	n/a
27	MAX	chr21:40176669-40177953	HUVEC	blood vessel:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
28	STAT3	chr21:40176556-40177115	MCF10A-Er-Src	breast:	n/a	chr21:40176858-40176869
29	HA-E2F1	chr21:40176753-40178798	MCF-7	breast:	n/a	chr21:40178507-40178517 chr21:40178473-40178483 chr21:40177209-40177226 chr21:40178322-40178331 chr21:40178104-40178114 chr21:40177212-40177223 chr21:40178219-40178228 chr21:40178529-40178540
30	MAFK	chr21:40176596-40177896	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr21:40176587-40176812	MCF-7	breast:	n/a	n/a
32	CTCF	chr21:40176680-40176830	Hela-S3	cervix:	n/a	n/a
33	IRF1	chr21:40176733-40178037	K562	blood:	n/a	chr21:40177557-40177571 chr21:40176857-40176870 chr21:40176856-40176870 chr21:40176754-40176767
34	REST	chr21:40176561-40178021	MCF-7	breast:	n/a	chr21:40177910-40177923 chr21:40177970-40177990 chr21:40177144-40177162
35	RAD21	chr21:40176514-40178069	MCF-7	breast:	n/a	chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178030-40178044
36	MAX	chr21:40176549-40178561	MCF-7	breast:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
37	CTCF	chr21:40176593-40176814	MCF-7	breast:	n/a	n/a
38	KAP1	chr21:40176699-40177469	U2OS	brain:	n/a	n/a
39	TAF1	chr21:40176755-40178130	MCF-7	breast:	n/a	n/a
40	MAX	chr21:40176739-40177987	A549	lung:	n/a	chr21:40177454-40177463 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
41	CTCF	chr21:40176720-40176870	HEEpiC	esophagus:	n/a	n/a
42	CHD1	chr21:40175807-40184420	IMR90	lung:	n/a	chr21:40183942-40183952
43	PML	chr21:40176703-40178141	MCF-7	breast:	n/a	n/a
44	HCFC1	chr21:40176304-40178467	Hela-S3	cervix:	n/a	n/a
45	RCOR1	chr21:40176543-40178074	K562	blood:	n/a	n/a
46	MAX	chr21:40176544-40178784	K562	blood:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
47	MAX	chr21:40176585-40178038	Hela-S3	cervix:	n/a	chr21:40176731-40176740 chr21:40177454-40177463 chr21:40176637-40176646 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
48	POLR2A	chr21:40176508-40178021	K562	blood:	n/a	n/a
49	RAD21	chr21:40176774-40177366	A549	lung:	n/a	chr21:40177096-40177109 chr21:40177093-40177112
50	RAD21	chr21:40176371-40180344	SK-N-SH	brain:	n/a	chr21:40178543-40178556 chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178101-40178114 chr21:40178124-40178136 chr21:40178030-40178044

No.	Distal block	Cell Line	Cell type
1	chr21:40176403..40178101-chr21:40218059..40219647,2	K562	blood:
2	chr21:40175328..40180167-chr21:40553641..40558387,7	K562	blood:
3	chr21:40105514..40106081-chr21:40176310..40177112,2	MCF-7	breast:
4	chr21:40175328..40178574-chr21:40554098..40556223,3	K562	blood:
5	chr21:40176416..40179104-chr21:40257484..40260730,3	MCF-7	breast:
6	chr21:40176632..40177186-chr21:40455915..40456479,2	MCF-7	breast:
7	chr21:40176662..40177180-chr21:40510094..40510804,2	MCF-7	breast:
8	chr21:40176601..40179515-chr21:40218059..40219886,2	K562	blood:
9	chr21:40174647..40179577-chr21:40285247..40287797,5	MCF-7	breast:
10	chr21:40176740..40177648-chr7:16685493..16686292,2	Hela-S3	cervix:
11	chr21:40176416..40178956-chr21:40498284..40502065,4	MCF-7	breast:
12	chr21:40176263..40179138-chr21:40817088..40818717,2	K562	blood:

Variant related genes	Relation type
ETS2	TF binding region
ENSG00000183527	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000228861	Chromatin interaction
ENSG00000136261	Chromatin interaction
ENSG00000234035	Chromatin interaction
ENSG00000229925	Chromatin interaction
ENSG00000229986	Chromatin interaction
ENSG00000185437	Chromatin interaction

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	nsv1058591	chr21:40114130-40190594	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv3430408	chr21:40176482-40179580	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40166600-40177000	Weak transcription	Gastric	stomach
2	chr21:40172000-40177000	Enhancers	HepG2	liver
3	chr21:40172600-40177200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr21:40175400-40177000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:40175400-40177000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:40175400-40177000	Enhancers	Esophagus	oesophagus
7	chr21:40175400-40177200	Enhancers	Lung	lung
8	chr21:40176000-40177000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr21:40176000-40177400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr21:40176000-40177600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr21:40176200-40177400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr21:40176400-40177000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr21:40176400-40177000	Flanking Active TSS	Hela-S3	cervix
14	chr21:40176400-40177200	Enhancers	Fetal Heart	heart
15	chr21:40176400-40177400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr21:40176400-40177400	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr21:40176400-40177400	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr21:40176400-40177400	Flanking Active TSS	NH-A	brain
19	chr21:40176400-40177600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:40176400-40177600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr21:40176600-40177000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr21:40176600-40177000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr21:40176600-40177000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
24	chr21:40176600-40177000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr21:40176600-40177000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr21:40176600-40177000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr21:40176600-40177000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr21:40176600-40177000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr21:40176600-40177000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr21:40176600-40177000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr21:40176600-40177000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr21:40176600-40177000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr21:40176600-40177000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr21:40176600-40177000	Flanking Active TSS	Liver	Liver
35	chr21:40176600-40177000	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
36	chr21:40176600-40177000	Enhancers	Left Ventricle	heart
37	chr21:40176600-40177000	Enhancers	Right Ventricle	heart
38	chr21:40176600-40177000	Enhancers	Spleen	Spleen
39	chr21:40176600-40177000	Enhancers	HMEC	breast
40	chr21:40176600-40177000	Enhancers	HSMMtube	muscle
41	chr21:40176600-40177000	Flanking Active TSS	NHEK	skin
42	chr21:40176600-40177200	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr21:40176600-40177200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr21:40176600-40177400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr21:40176600-40177400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr21:40176600-40177400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr21:40176600-40177400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr21:40176600-40177400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr21:40176600-40177400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr21:40176600-40177400	Flanking Active TSS	Fetal Intestine Large	intestine

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