Variant report

Variant	rs555096971
Chromosome Location	chr21:40684523-40684524
allele	A/C
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	ELF1	chr21:40684315-40684675	K562	blood:	n/a	n/a
2	TBL1XR1	chr21:40683908-40684601	K562	blood:	n/a	n/a
3	POLR2A	chr21:40684297-40684753	K562	blood:	n/a	n/a
4	CHD2	chr21:40684163-40684617	H1-hESC	embryonic stem cell:	n/a	n/a
5	GATA3	chr21:40683869-40684721	SK-N-SH	brain:	n/a	n/a
6	HMGN3	chr21:40684280-40684672	K562	blood:	n/a	n/a
7	TBP	chr21:40684025-40684539	GM12878	blood:	n/a	n/a
8	ZBTB7A	chr21:40684293-40684802	ECC-1	luminal epithelium:	n/a	n/a
9	STAT3	chr21:40684196-40684537	GM12878	blood:	n/a	n/a
10	SP4	chr21:40684228-40684572	H1-hESC	embryonic stem cell:	n/a	n/a
11	YY1	chr21:40684301-40684688	GM12892	blood:	n/a	n/a
12	POU2F2	chr21:40684195-40684523	GM12891	blood:	n/a	chr21:40684235-40684248
13	POLR2A	chr21:40684358-40684615	H1-hESC	embryonic stem cell:	n/a	n/a
14	IRF3	chr21:40684248-40684557	Hela-S3	cervix:	n/a	n/a
15	GATA3	chr21:40683843-40684644	SK-N-SH	brain:	n/a	n/a
16	HEY1	chr21:40684072-40684844	K562	blood:	n/a	n/a
17	EGR1	chr21:40684202-40684806	MCF-7	breast:	n/a	chr21:40684474-40684487 chr21:40684475-40684485 chr21:40684443-40684450 chr21:40684475-40684486 chr21:40684473-40684488 chr21:40684474-40684487 chr21:40684475-40684484 chr21:40684471-40684485
18	SIN3AK20	chr21:40684015-40687111	MCF-7	breast:	n/a	n/a
19	ELF1	chr21:40684185-40684676	K562	blood:	n/a	n/a
20	ZNF384	chr21:40684214-40684614	K562	blood:	n/a	n/a
21	POLR2A	chr21:40684347-40686942	K562	blood:	n/a	n/a
22	EP300	chr21:40684338-40684536	GM12878	blood:	n/a	n/a
23	SP1	chr21:40684125-40684700	A549	lung:	n/a	chr21:40684390-40684411 chr21:40684472-40684482 chr21:40684371-40684380 chr21:40684472-40684482
24	MAX	chr21:40684177-40684904	MCF-7	breast:	n/a	n/a
25	MXI1	chr21:40683978-40684684	GM12878	blood:	n/a	n/a
26	POLR2A	chr21:40684348-40684683	K562	blood:	n/a	n/a
27	ELK1	chr21:40684376-40684534	Hela-S3	cervix:	n/a	n/a
28	JUND	chr21:40684378-40684531	HepG2	liver:	n/a	chr21:40684393-40684402
29	SP1	chr21:40684121-40684610	H1-hESC	embryonic stem cell:	n/a	chr21:40684390-40684411 chr21:40684472-40684482 chr21:40684371-40684380 chr21:40684472-40684482
30	REST	chr21:40683818-40686869	H1-neurons	neurons:	n/a	chr21:40685323-40685336
31	YY1	chr21:40684205-40684668	GM12878	blood:	n/a	n/a
32	HDAC2	chr21:40684320-40684542	K562	blood:	n/a	n/a
33	MAX	chr21:40684289-40684678	K562	blood:	n/a	n/a
34	BRCA1	chr21:40684271-40684587	Hela-S3	cervix:	n/a	n/a
35	MYC	chr21:40684224-40684681	K562	blood:	n/a	n/a
36	TBP	chr21:40684242-40684589	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr21:40684305-40684748	K562	blood:	n/a	n/a
38	RFX5	chr21:40684203-40684629	Hela-S3	cervix:	n/a	chr21:40684392-40684401
39	SP1	chr21:40684113-40684666	GM12878	blood:	n/a	chr21:40684390-40684411 chr21:40684472-40684482 chr21:40684371-40684380 chr21:40684472-40684482
40	POLR2A	chr21:40684380-40686835	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr21:40684324-40686793	GM12892	blood:	n/a	n/a
42	MYC	chr21:40684386-40684527	MCF-7	breast:	n/a	n/a
43	CREB1	chr21:40684268-40684814	GM12878	blood:	n/a	n/a
44	POLR2A	chr21:40684267-40686937	GM18505	blood:	n/a	n/a
45	NFYA	chr21:40684227-40684600	GM12878	blood:	n/a	chr21:40684389-40684404 chr21:40684389-40684403 chr21:40684389-40684407 chr21:40684389-40684404
46	GATA3	chr21:40683901-40684805	MCF-7	breast:	n/a	n/a
47	MYC	chr21:40684275-40684833	NB4	blood:	n/a	n/a
48	RCOR1	chr21:40684094-40684549	GM12878	blood:	n/a	n/a
49	CHD2	chr21:40684384-40684611	HepG2	liver:	n/a	n/a
50	MAFK	chr21:40684253-40684551	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
2	chr21:40554013..40557423-chr21:40684520..40688084,3	MCF-7	breast:
3	chr21:37527438..37529025-chr21:40684261..40686264,2	MCF-7	breast:
4	chr21:40684209..40686276-chr21:40817224..40819799,4	MCF-7	breast:
5	chr21:40682124..40685118-chr21:40763752..40765296,2	K562	blood:
6	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
7	chr21:40683717..40685708-chr21:40747929..40750593,3	MCF-7	breast:
8	chr21:40683837..40687545-chr21:40816624..40819639,6	K562	blood:
9	chr21:40681416..40687854-chr21:40744378..40751195,8	K562	blood:
10	chr1:204379398..204382038-chr21:40683560..40686325,2	MCF-7	breast:
11	chr21:40554270..40557456-chr21:40682408..40685088,3	K562	blood:
12	chr21:40683876..40687631-chr21:40749667..40753921,6	K562	blood:
13	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
14	chr21:40684445..40685036-chr3:160283085..160283851,2	Hela-S3	cervix:
15	chr21:40684466..40689800-chr21:40758261..40763098,10	K562	blood:
16	chr21:40683731..40685549-chr21:40816150..40817682,2	MCF-7	breast:
17	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
18	chr21:40555032..40557155-chr21:40684133..40685858,2	MCF-7	breast:
19	chr21:40550424..40553042-chr21:40683249..40686279,3	K562	blood:
20	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
21	chr21:40683489..40689074-chr21:40750757..40754639,9	MCF-7	breast:
22	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
23	chr21:40684444..40687629-chr3:63848425..63851169,6	MCF-7	breast:
24	chr21:40684138..40686385-chr9:131445458..131447217,2	MCF-7	breast:
25	chr21:40684107..40685647-chr21:40816624..40819498,2	K562	blood:
26	chr21:40553454..40557456-chr21:40682892..40687176,12	K562	blood:

Variant related genes	Relation type
BRWD1-AS1	TF binding region
ENSG00000227406	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000158615	Chromatin interaction
ENSG00000119335	Chromatin interaction
ENSG00000236830	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000163635	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000238556	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000163634	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	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
5	esv3439649	chr21:40683507-40687455	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	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
7	nsv587482	chr21:40684427-40706594	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 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	chr21:40673600-40684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40683600-40686600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr21:40683800-40685400	Active TSS	Right Atrium	heart
4	chr21:40683800-40686400	Active TSS	Thymus	Thymus
5	chr21:40684000-40685800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr21:40684000-40686200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr21:40684000-40686200	Active TSS	Fetal Thymus	thymus
8	chr21:40684000-40686400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr21:40684000-40686400	Active TSS	Right Ventricle	heart
10	chr21:40684000-40686600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr21:40684000-40686600	Active TSS	Aorta	Aorta
12	chr21:40684000-40686600	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr21:40684200-40684600	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr21:40684200-40685000	Active TSS	Brain Germinal Matrix	brain
15	chr21:40684200-40685600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr21:40684200-40686000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr21:40684200-40686000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr21:40684200-40686000	Active TSS	Placenta Amnion	Placenta Amnion
19	chr21:40684200-40686000	Active TSS	HepG2	liver
20	chr21:40684200-40686200	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr21:40684200-40686200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr21:40684200-40686200	Active TSS	Brain Anterior Caudate	brain
23	chr21:40684200-40686200	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr21:40684200-40686400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr21:40684200-40686400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:40684200-40686400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr21:40684200-40686400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr21:40684200-40686400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr21:40684200-40686400	Active TSS	Brain Cingulate Gyrus	brain
30	chr21:40684200-40686400	Active TSS	Fetal Brain Female	brain
31	chr21:40684200-40686400	Active TSS	Pancreas	Pancrea
32	chr21:40684200-40686400	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr21:40684200-40686400	Active TSS	GM12878-XiMat	blood
34	chr21:40684200-40686600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr21:40684200-40686600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr21:40684200-40686600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr21:40684200-40686600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr21:40684200-40686600	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr21:40684200-40686600	Active TSS	Fetal Intestine Large	intestine
40	chr21:40684200-40686600	Active TSS	Fetal Intestine Small	intestine
41	chr21:40684200-40686600	Active TSS	Fetal Stomach	stomach
42	chr21:40684200-40686600	Active TSS	Left Ventricle	heart
43	chr21:40684200-40686600	Active TSS	Ovary	ovary
44	chr21:40684200-40686600	Active TSS	Psoas Muscle	Psoas
45	chr21:40684200-40686600	Active TSS	Stomach Smooth Muscle	stomach
46	chr21:40684200-40686600	Active TSS	HSMM	muscle
47	chr21:40684200-40686800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr21:40684200-40686800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr21:40684400-40684600	Active TSS	Primary B cells from cord blood	blood
50	chr21:40684400-40684600	Active TSS	Primary T helper naive cells from peripheral blood	blood

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