Variant report

Variant	rs112890961
Chromosome Location	chr21:40555115-40555116
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	MYC	chr21:40555087-40555544	H1-hESC	embryonic stem cell:	n/a	chr21:40555316-40555325
2	POLR2A	chr21:40554888-40556110	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr21:40554959-40555916	ECC-1	luminal epithelium:	n/a	chr21:40555869-40555885
4	E2F6	chr21:40555072-40555637	A549	lung:	n/a	n/a
5	USF2	chr21:40554746-40555786	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr21:40554989-40556193	HUVEC	blood vessel:	n/a	n/a
7	TAF1	chr21:40554575-40556243	MCF-7	breast:	n/a	n/a
8	MAX	chr21:40554449-40556159	K562	blood:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
9	YY1	chr21:40554889-40556121	GM12892	blood:	n/a	chr21:40555795-40555806 chr21:40556007-40556016
10	CEBPD	chr21:40554774-40556157	K562	blood:	n/a	n/a
11	POLR2A	chr21:40554769-40556234	H1-neurons	neurons:	n/a	n/a
12	ELF1	chr21:40554679-40556142	GM12878	blood:	n/a	n/a
13	USF1	chr21:40555092-40555755	SK-N-SH	brain:	n/a	n/a
14	BRCA1	chr21:40554764-40556046	Hela-S3	cervix:	n/a	n/a
15	FOXM1	chr21:40554836-40556178	MCF-7	breast:	n/a	n/a
16	PML	chr21:40554921-40556323	MCF-7	breast:	n/a	n/a
17	POLR2A	chr21:40554922-40556221	HUVEC	blood vessel:	n/a	n/a
18	YY1	chr21:40555030-40556161	GM12878	blood:	n/a	chr21:40555795-40555806 chr21:40556007-40556016
19	MAX	chr21:40554534-40556257	MCF-7	breast:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
20	ZNF274	chr21:40554952-40555538	K562	blood:	n/a	n/a
21	POLR2A	chr21:40554929-40556187	ECC-1	luminal epithelium:	n/a	n/a
22	YY1	chr21:40555013-40555969	SK-N-SH_RA	brain:	n/a	chr21:40555795-40555806
23	MXI1	chr21:40554987-40556140	Hela-S3	cervix:	n/a	n/a
24	MYC	chr21:40555082-40555548	GM12878	blood:	n/a	chr21:40555316-40555325
25	MAX	chr21:40554104-40556218	NB4	blood:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
26	TRIM28	chr21:40554973-40556051	K562	blood:	n/a	n/a
27	MAX	chr21:40555106-40555959	HUVEC	blood vessel:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
28	TAF1	chr21:40554746-40556191	ECC-1	luminal epithelium:	n/a	n/a
29	HDAC2	chr21:40554592-40556281	MCF-7	breast:	n/a	chr21:40555466-40555475
30	SIN3AK20	chr21:40554971-40555441	K562	blood:	n/a	n/a
31	TAF7	chr21:40554880-40555618	H1-hESC	embryonic stem cell:	n/a	n/a
32	JUND	chr21:40554629-40556282	MCF-7	breast:	n/a	chr21:40555407-40555416 chr21:40555482-40555491
33	MAX	chr21:40554608-40556254	ECC-1	luminal epithelium:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
34	POLR2A	chr21:40555044-40555596	HepG2	liver:	n/a	n/a
35	E2F6	chr21:40554707-40555610	K562	blood:	n/a	n/a
36	MAX	chr21:40554952-40556039	H1-hESC	embryonic stem cell:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
37	TBP	chr21:40554331-40556457	K562	blood:	n/a	n/a
38	MAX	chr21:40554338-40556187	Hela-S3	cervix:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
39	BACH1	chr21:40554695-40555957	H1-hESC	embryonic stem cell:	n/a	n/a
40	YY1	chr21:40554697-40556135	K562	blood:	n/a	chr21:40555795-40555806 chr21:40556007-40556016
41	POLR2A	chr21:40554781-40556177	MCF-7	breast:	n/a	n/a
42	CCNT2	chr21:40554730-40556279	K562	blood:	n/a	n/a
43	MYC	chr21:40554007-40556427	K562	blood:	n/a	chr21:40555812-40555822 chr21:40555316-40555325
44	TCF3	chr21:40555097-40555381	GM12878	blood:	n/a	n/a
45	POLR2A	chr21:40554254-40556348	Hela-S3	cervix:	n/a	n/a
46	RELA	chr21:40555102-40556066	GM19099	blood:	n/a	n/a
47	TCF7L2	chr21:40554941-40556120	HCT-116	colon:	n/a	n/a
48	CEBPD	chr21:40555024-40556118	K562	blood:	n/a	n/a
49	RUNX3	chr21:40554698-40556180	GM12878	blood:	n/a	n/a
50	POLR2A	chr21:40554900-40556162	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
2	chr21:40554206..40555769-chr21:40571633..40573834,2	K562	blood:
3	chr21:40552516..40555515-chr21:40758943..40760790,2	MCF-7	breast:
4	chr21:40552682..40557546-chr21:40815502..40820280,12	K562	blood:
5	chr21:40555015..40555947-chr4:25314153..25314779,2	NB4	blood:
6	chr21:40553821..40557385-chr21:40719764..40724370,6	K562	blood:
7	chr21:40554325..40556073-chr21:40808791..40811765,2	K562	blood:
8	chr21:40552682..40557091-chr21:40814575..40819975,14	K562	blood:
9	chr21:40554651..40557222-chr21:40599686..40602201,3	K562	blood:
10	chr21:40175328..40178574-chr21:40554098..40556223,3	K562	blood:
11	chr21:40554460..40556456-chr21:40823248..40825971,3	K562	blood:
12	chr21:40554013..40557423-chr21:40684520..40688084,3	MCF-7	breast:
13	chr21:40554955..40557163-chr21:40823681..40826162,2	K562	blood:
14	chr21:40553901..40555576-chr21:40760955..40763916,2	K562	blood:
15	chr12:99038540..99039458-chr21:40555041..40555555,2	Hela-S3	cervix:
16	chr21:40555099..40556872-chr21:40718336..40720047,2	MCF-7	breast:
17	chr21:40552621..40555799-chr21:40758034..40760615,3	K562	blood:
18	chr21:40554663..40558370-chr21:40719503..40722190,4	MCF-7	breast:
19	chr21:40175328..40180167-chr21:40553641..40558387,7	K562	blood:
20	chr21:40552640..40555791-chr21:40749339..40752310,3	K562	blood:
21	chr21:40554637..40556936-chr21:40588612..40590641,2	K562	blood:
22	chr21:40553976..40556398-chr21:40816228..40819085,2	MCF-7	breast:
23	chr21:40553454..40557456-chr21:40682892..40687176,12	K562	blood:
24	chr21:40555032..40557155-chr21:40684133..40685858,2	MCF-7	breast:
25	chr21:40032723..40034705-chr21:40552796..40555245,2	MCF-7	breast:
26	chr21:40551398..40560769-chr21:40565658..40576445,18	K562	blood:

Variant related genes	Relation type
PSMG1	TF binding region
ENSG00000272991	TF binding region
ENSG00000185437	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000120868	Chromatin interaction
ENSG00000157554	Chromatin interaction
ENSG00000168228	Chromatin interaction
ENSG00000166130	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000238141	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv3422692	chr21:40554107-40556955	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	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	chr21:40553000-40556600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr21:40553600-40557200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr21:40553800-40555200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr21:40553800-40556200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr21:40553800-40557000	Active TSS	GM12878-XiMat	blood
6	chr21:40554000-40555200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr21:40554000-40555200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr21:40554000-40555200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr21:40554000-40555200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr21:40554000-40556400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr21:40554000-40556400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr21:40554000-40556600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr21:40554000-40556600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr21:40554000-40556600	Active TSS	Colonic Mucosa	Colon
15	chr21:40554000-40556600	Active TSS	Fetal Muscle Trunk	muscle
16	chr21:40554000-40556600	Active TSS	A549	lung
17	chr21:40554000-40556800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr21:40554000-40557200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr21:40554200-40555200	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr21:40554200-40555200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr21:40554200-40556200	Active TSS	Esophagus	oesophagus
22	chr21:40554200-40556200	Active TSS	Lung	lung
23	chr21:40554200-40556200	Active TSS	Pancreas	Pancrea
24	chr21:40554200-40556400	Active TSS	Psoas Muscle	Psoas
25	chr21:40554200-40556600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr21:40554200-40556600	Active TSS	Right Ventricle	heart
27	chr21:40554400-40555200	Active TSS	Brain Germinal Matrix	brain
28	chr21:40554400-40556200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr21:40554400-40556200	Active TSS	Brain Anterior Caudate	brain
30	chr21:40554400-40556200	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr21:40554400-40556400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr21:40554400-40556400	Active TSS	Colon Smooth Muscle	Colon
33	chr21:40554400-40556400	Active TSS	Ovary	ovary
34	chr21:40554400-40556400	Active TSS	Hela-S3	cervix
35	chr21:40554400-40556400	Active TSS	HUVEC	blood vessel
36	chr21:40554400-40556600	Active TSS	H1 Cell Line	embryonic stem cell
37	chr21:40554400-40556600	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr21:40554400-40556600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr21:40554400-40556600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr21:40554400-40556600	Active TSS	Aorta	Aorta
41	chr21:40554400-40556600	Active TSS	Brain Cingulate Gyrus	brain
42	chr21:40554400-40556600	Active TSS	Placenta	Placenta
43	chr21:40554400-40556600	Active TSS	Placenta Amnion	Placenta Amnion
44	chr21:40554400-40556600	Active TSS	HSMMtube	muscle
45	chr21:40554400-40556600	Active TSS	NHDF-Ad	bronchial
46	chr21:40554400-40556600	Active TSS	NHEK	skin
47	chr21:40554400-40556800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr21:40554400-40556800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr21:40554400-40556800	Active TSS	Fetal Intestine Large	intestine
50	chr21:40554400-40556800	Active TSS	NHLF	lung

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