Variant report

Variant	rs554928612
Chromosome Location	chr21:40720024-40720025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr21:40716967-40721099	SK-N-SH	brain:	n/a	n/a
2	YY1	chr21:40719940-40721055	GM12878	blood:	n/a	n/a
3	POLR2A	chr21:40719451-40723014	GM12878	blood:	n/a	n/a
4	REST	chr21:40719476-40722011	H1-neurons	neurons:	n/a	chr21:40721572-40721585 chr21:40721572-40721585
5	POLR2A	chr21:40716164-40723345	K562	blood:	n/a	n/a
6	E2F4	chr21:40719770-40721703	MCF10A-Er-Src	breast:	n/a	chr21:40720601-40720612 chr21:40721328-40721337 chr21:40721584-40721593 chr21:40721170-40721179
7	SIN3AK20	chr21:40719291-40722472	MCF-7	breast:	n/a	n/a
8	MXI1	chr21:40719317-40721951	IMR90	lung:	n/a	n/a
9	POLR2A	chr21:40719983-40722069	GM12878	blood:	n/a	n/a
10	MYC	chr21:40719529-40722622	K562	blood:	n/a	n/a
11	POLR2A	chr21:40719978-40721123	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr21:40719377-40722068	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD1	chr21:40719934-40720638	GM12878	blood:	n/a	n/a
14	TBL1XR1	chr21:40718919-40720642	K562	blood:	n/a	n/a
15	IRF1	chr21:40718316-40720432	K562	blood:	n/a	n/a
16	ARID3A	chr21:40719952-40720347	HepG2	liver:	n/a	n/a
17	POLR2A	chr21:40719962-40721926	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr21:40719412-40723072	GM12891	blood:	n/a	n/a
19	POLR2A	chr21:40720015-40721055	K562	blood:	n/a	n/a
20	SIN3A	chr21:40719531-40721032	H1-hESC	embryonic stem cell:	n/a	n/a
21	IRF1	chr21:40718834-40720511	K562	blood:	n/a	n/a
22	POLR2A	chr21:40719975-40721071	GM12878	blood:	n/a	n/a
23	MYC	chr21:40719706-40720199	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr21:40719490-40723323	GM12878	blood:	n/a	n/a
25	CHD1	chr21:40719664-40720447	H1-hESC	embryonic stem cell:	n/a	n/a
26	SIN3AK20	chr21:40719491-40720761	MCF-7	breast:	n/a	n/a
27	MAFK	chr21:40719514-40720314	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr21:40719984-40720041	MCF-7	breast:	n/a	n/a
29	MAFK	chr21:40720017-40720520	K562	blood:	n/a	n/a
30	YY1	chr21:40720002-40720265	GM12892	blood:	n/a	n/a
31	YY1	chr21:40720021-40720483	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr21:40719476-40720093	K562	blood:	n/a	n/a
33	UBTF	chr21:40719567-40721068	K562	blood:	n/a	n/a
34	POLR2A	chr21:40719461-40723355	K562	blood:	n/a	n/a
35	TBP	chr21:40719557-40722613	K562	blood:	n/a	n/a
36	YY1	chr21:40720020-40720355	SK-N-SH_RA	brain:	n/a	n/a
37	YY1	chr21:40720024-40720393	GM12891	blood:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24607940..24610732-chr21:40718347..40720759,2	MCF-7	breast:
2	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
3	chr20:49347681..49350459-chr21:40719549..40721947,2	MCF-7	breast:
4	chr21:40685861..40686376-chr21:40719745..40720551,2	MCF-7	breast:
5	chr21:40718950..40720909-chr8:144820152..144822605,2	MCF-7	breast:
6	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
7	chr21:40716662..40723444-chr21:40748337..40754328,16	MCF-7	breast:
8	chr21:40635414..40638745-chr21:40717382..40720310,3	K562	blood:
9	chr21:40719359..40724848-chr21:40748806..40754741,7	MCF-7	breast:
10	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
11	chr21:40650313..40652723-chr21:40719146..40721312,2	MCF-7	breast:
12	chr21:40719979..40722729-chr21:40816056..40819504,5	MCF-7	breast:
13	chr21:40719750..40724652-chr21:40748317..40754270,9	K562	blood:
14	chr21:40555099..40556872-chr21:40718336..40720047,2	MCF-7	breast:
15	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
16	chr21:40553821..40557385-chr21:40719764..40724370,6	K562	blood:
17	chr21:40719238..40723494-chr21:40813785..40819496,7	MCF-7	breast:
18	chr21:40716961..40722807-chr21:40750720..40754894,10	K562	blood:
19	chr21:40719170..40722188-chr21:40780437..40783108,3	MCF-7	breast:
20	chr21:40719410..40723060-chr21:40814028..40819084,9	K562	blood:
21	chr21:40719273..40720815-chr21:40782667..40784260,2	K562	blood:
22	chr21:40554663..40558370-chr21:40719503..40722190,4	MCF-7	breast:
23	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238556	TF binding region
HMGN1	TF binding region
ENSG00000255568	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000203499	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000259321	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000183527	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	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv3439352	chr21:40719607-40722455	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	25 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	chr21:40717000-40720400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr21:40717200-40720200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
3	chr21:40717400-40720200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr21:40717400-40720400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
5	chr21:40717600-40720200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40717600-40720400	Transcr. at gene 5' and 3'	A549	lung
7	chr21:40717600-40720400	Transcr. at gene 5' and 3'	K562	blood
8	chr21:40717800-40720200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr21:40718000-40721400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr21:40718200-40720400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
11	chr21:40718400-40720400	Active TSS	Right Atrium	heart
12	chr21:40718800-40720200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr21:40718800-40720400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr21:40718800-40721400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr21:40718800-40721600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr21:40718800-40721600	Active TSS	Brain Germinal Matrix	brain
17	chr21:40718800-40721600	Active TSS	Fetal Stomach	stomach
18	chr21:40718800-40721800	Active TSS	Fetal Intestine Large	intestine
19	chr21:40718800-40721800	Active TSS	Fetal Intestine Small	intestine
20	chr21:40718800-40722000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr21:40718800-40722200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr21:40718800-40722200	Active TSS	GM12878-XiMat	blood
23	chr21:40719000-40720400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr21:40719000-40721600	Active TSS	HMEC	breast
25	chr21:40719000-40722200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr21:40719000-40722400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr21:40719200-40720200	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr21:40719200-40720400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr21:40719200-40722000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr21:40719200-40722000	Active TSS	Fetal Brain Female	brain
31	chr21:40719200-40722000	Active TSS	HSMM	muscle
32	chr21:40719200-40722000	Active TSS	HSMMtube	muscle
33	chr21:40719200-40722200	Active TSS	Fetal Kidney	kidney
34	chr21:40719200-40722400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr21:40719200-40722800	Active TSS	Hela-S3	cervix
36	chr21:40719400-40720200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr21:40719400-40720200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr21:40719400-40720400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr21:40719400-40721400	Active TSS	Primary T cells fromperipheralblood	blood
40	chr21:40719400-40721600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr21:40719400-40721600	Active TSS	Fetal Muscle Trunk	muscle
42	chr21:40719400-40721800	Active TSS	Ovary	ovary
43	chr21:40719400-40721800	Active TSS	Right Ventricle	heart
44	chr21:40719400-40722000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr21:40719400-40722200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr21:40719400-40722200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr21:40719400-40722400	Active TSS	H9 Cell Line	embryonic stem cell
48	chr21:40719400-40722600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr21:40719600-40720200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr21:40719600-40720200	Flanking Active TSS	Liver	Liver

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