Variant report

Variant	rs562904252
Chromosome Location	chr21:40177739-40177740
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	MAX	chr21:40176897-40178012	ECC-1	luminal epithelium:	n/a	chr21:40177454-40177463 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
2	MXI1	chr21:40176328-40180482	SK-N-SH	brain:	n/a	chr21:40176631-40176646 chr21:40176633-40176648
3	POLR2A	chr21:40177255-40178143	PFSK-1	brain:	n/a	n/a
4	MAX	chr21:40176914-40178092	SK-N-SH	brain:	n/a	chr21:40177454-40177463 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
5	GTF2F1	chr21:40176834-40178025	Hela-S3	cervix:	n/a	n/a
6	TAF1	chr21:40177721-40177943	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr21:40177362-40178067	GM19099	blood:	n/a	n/a
8	CTCF	chr21:40177733-40178422	IMR90	lung:	n/a	chr21:40177982-40177995
9	TAF1	chr21:40177620-40178004	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr21:40175826-40184443	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr21:40177673-40177905	GM12878	blood:	n/a	n/a
12	ZBTB7A	chr21:40177330-40178722	K562	blood:	n/a	chr21:40178114-40178125
13	POLR2A	chr21:40177687-40178075	HepG2	liver:	n/a	n/a
14	MYC	chr21:40176800-40178471	NB4	blood:	n/a	chr21:40177454-40177463 chr21:40178111-40178121 chr21:40177455-40177462 chr21:40177836-40177845 chr21:40177456-40177465
15	REST	chr21:40177713-40177987	A549	lung:	n/a	chr21:40177910-40177923
16	PML	chr21:40177352-40178105	K562	blood:	n/a	n/a
17	RAD21	chr21:40176494-40178046	ECC-1	luminal epithelium:	n/a	chr21:40177096-40177109 chr21:40177093-40177112 chr21:40178030-40178044
18	POLR2A	chr21:40177653-40178081	GM12891	blood:	n/a	n/a
19	SIN3AK20	chr21:40177683-40177978	PFSK-1	brain:	n/a	n/a
20	ETS1	chr21:40177243-40178427	K562	blood:	n/a	chr21:40177857-40177864 chr21:40178232-40178241 chr21:40177544-40177553
21	TCF7L2	chr21:40176617-40177947	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr21:40177100-40180919	PBDE	blood:	n/a	n/a
23	ZNF384	chr21:40177020-40177876	K562	blood:	n/a	n/a
24	YY1	chr21:40177436-40178046	ECC-1	luminal epithelium:	n/a	chr21:40177982-40177996 chr21:40178021-40178035 chr21:40177948-40177962
25	FOXP2	chr21:40177342-40178054	PFSK-1	brain:	n/a	n/a
26	EP300	chr21:40177357-40177990	HepG2	liver:	n/a	n/a
27	POLR2A	chr21:40177320-40178063	GM10847	blood:	n/a	n/a
28	POLR2A	chr21:40176831-40178983	HL-60	blood:	n/a	n/a
29	TBP	chr21:40177071-40178406	K562	blood:	n/a	n/a
30	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
31	POLR2A	chr21:40177202-40178325	A549	lung:	n/a	n/a
32	CCNT2	chr21:40176993-40179135	K562	blood:	n/a	n/a
33	TCF12	chr21:40176681-40178155	A549	lung:	n/a	n/a
34	HEY1	chr21:40177252-40178132	K562	blood:	n/a	chr21:40177985-40178000 chr21:40178067-40178082 chr21:40178106-40178121
35	POLR2A	chr21:40177466-40178103	H1-hESC	embryonic stem cell:	n/a	n/a
36	TBL1XR1	chr21:40176988-40177899	K562	blood:	n/a	n/a
37	CTCF	chr21:40177720-40177870	MCF-7	breast:	n/a	n/a
38	POLR2A	chr21:40177116-40178153	U87	brain:	n/a	n/a
39	GABPA	chr21:40177240-40178451	K562	blood:	n/a	chr21:40177452-40177461 chr21:40178026-40178035 chr21:40177988-40177997 chr21:40178322-40178331
40	POLR2A	chr21:40177260-40178541	NB4	blood:	n/a	n/a
41	POLR2A	chr21:40177296-40178259	GM15510	blood:	n/a	n/a
42	POLR2A	chr21:40177252-40178085	HEK293	kidney:	n/a	n/a
43	ZKSCAN1	chr21:40176931-40177978	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr21:40177060-40178136	K562	blood:	n/a	n/a
45	ELK1	chr21:40177383-40177826	GM12878	blood:	n/a	n/a
46	POLR2A	chr21:40176818-40178228	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr21:40177052-40178113	PFSK-1	brain:	n/a	n/a
48	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
49	TEAD4	chr21:40177192-40178063	K562	blood:	n/a	n/a
50	CEBPD	chr21:40177389-40178099	HepG2	liver:	n/a	n/a

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	chr21:40175328..40178574-chr21:40554098..40556223,3	K562	blood:
4	chr21:40176416..40179104-chr21:40257484..40260730,3	MCF-7	breast:
5	chr21:40113948..40115514-chr21:40177430..40179064,2	K562	blood:
6	chr21:40176601..40179515-chr21:40218059..40219886,2	K562	blood:
7	chr21:40174647..40179577-chr21:40285247..40287797,5	MCF-7	breast:
8	chr11:67249840..67250624-chr21:40177263..40178201,2	Hela-S3	cervix:
9	chr1:210546726..210547661-chr21:40176943..40177887,2	Hela-S3	cervix:
10	chr21:40177627..40180426-chr21:40542526..40544967,2	K562	blood:
11	chr21:40177082..40177855-chr9:125666873..125667749,2	Hela-S3	cervix:
12	chr21:40177696..40178382-chr3:121467811..121468789,2	Hela-S3	cervix:
13	chr21:40176416..40178956-chr21:40498284..40502065,4	MCF-7	breast:
14	chr17:59940341..59941197-chr21:40177450..40178230,2	Hela-S3	cervix:
15	chr16:2205045..2205567-chr21:40177575..40178112,2	Hela-S3	cervix:
16	chr21:40176263..40179138-chr21:40817088..40818717,2	K562	blood:
17	chr21:40177663..40178343-chr6:27113539..27114763,3	Hela-S3	cervix:
18	chr21:40177189..40177905-chr5:108744975..108745566,2	Hela-S3	cervix:

Variant related genes	Relation type
ETS2	TF binding region
ENSG00000136492	Chromatin interaction
ENSG00000223806	Chromatin interaction
ENSG00000110711	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000229925	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000056586	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000228861	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000234035	Chromatin interaction
ENSG00000173230	Chromatin interaction
ENSG00000198961	Chromatin interaction
ENSG00000229986	Chromatin interaction
ENSG00000235701	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40176600-40179800	Active TSS	Rectal Smooth Muscle	rectum
2	chr21:40176600-40180400	Active TSS	Ovary	ovary
3	chr21:40176600-40181600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr21:40176600-40182000	Active TSS	Brain Anterior Caudate	brain
5	chr21:40176800-40177800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr21:40176800-40177800	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr21:40176800-40179200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr21:40176800-40179200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr21:40176800-40179200	Active TSS	Stomach Mucosa	stomach
10	chr21:40176800-40179600	Active TSS	Psoas Muscle	Psoas
11	chr21:40176800-40179600	Active TSS	A549	lung
12	chr21:40176800-40179800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr21:40176800-40179800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr21:40176800-40180000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr21:40176800-40180000	Active TSS	Aorta	Aorta
16	chr21:40176800-40180000	Active TSS	Fetal Kidney	kidney
17	chr21:40176800-40180000	Active TSS	Thymus	Thymus
18	chr21:40176800-40180400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:40176800-40180600	Active TSS	Brain Substantia Nigra	brain
20	chr21:40176800-40181000	Active TSS	Brain Angular Gyrus	brain
21	chr21:40176800-40182800	Active TSS	Brain Cingulate Gyrus	brain
22	chr21:40176800-40182800	Active TSS	Brain Hippocampus Middle	brain
23	chr21:40177000-40178200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr21:40177000-40178400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr21:40177000-40178600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr21:40177000-40178600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr21:40177000-40178800	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr21:40177000-40178800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr21:40177000-40178800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
30	chr21:40177000-40178800	Active TSS	HSMM	muscle
31	chr21:40177000-40179000	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr21:40177000-40179000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr21:40177000-40179200	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr21:40177000-40179200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr21:40177000-40179200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr21:40177000-40179400	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr21:40177000-40179600	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr21:40177000-40179600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr21:40177000-40179600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr21:40177000-40179600	Active TSS	Colon Smooth Muscle	Colon
41	chr21:40177000-40179800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr21:40177000-40179800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr21:40177000-40179800	Active TSS	Liver	Liver
44	chr21:40177000-40179800	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr21:40177000-40180000	Active TSS	Esophagus	oesophagus
46	chr21:40177000-40180600	Active TSS	Gastric	stomach
47	chr21:40177000-40180600	Active TSS	Small Intestine	intestine
48	chr21:40177000-40181400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr21:40177200-40178000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr21:40177200-40178400	Active TSS	Primary T cells from cord blood	blood

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