Variant report

Variant	rs544755540
Chromosome Location	chr21:40984609-40984610
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	YY1	chr21:40984431-40984953	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3AK20	chr21:40984404-40985021	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr21:40983415-40985718	H1-hESC	embryonic stem cell:	n/a	chr21:40984977-40984990
4	JUND	chr21:40984189-40984902	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr21:40984561-40985053	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr21:40984450-40984819	SK-N-SH_RA	brain:	n/a	n/a
7	CTBP2	chr21:40984082-40984890	H1-hESC	embryonic stem cell:	n/a	n/a
8	TAF1	chr21:40984585-40984991	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr21:40984118-40985144	H1-hESC	embryonic stem cell:	n/a	chr21:40984906-40984916
10	TAF1	chr21:40984435-40985023	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr21:40984201-40985024	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr21:40984091-40985223	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr21:40984411-40984864	H1-hESC	embryonic stem cell:	n/a	n/a
14	NRF1	chr21:40984575-40985199	SK-N-SH	brain:	n/a	chr21:40984921-40984930 chr21:40984814-40984823
15	ZNF143	chr21:40984112-40984851	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr21:40984527-40985028	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr21:40984474-40984791	SK-N-SH_RA	brain:	n/a	n/a
18	POLR2A	chr21:40984551-40985170	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF263	chr21:40984604-40984968	HEK293-T-REx	kidney:	n/a	chr21:40984822-40984831

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf88-1	chr21:40984224-40984994	NONHSAT082200
2	lnc-C21orf88-1	chr21:40984224-40984749	NR_026542
3	lnc-C21orf88-1	chr21:40984224-40984749	NR_026543

Variant related genes	Relation type
C21orf88	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv11702	chr21:40981640-40987483	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv587484	chr21:40983133-40986120	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40982800-40985200	Active TSS	Rectal Mucosa Donor 31	rectum
2	chr21:40982800-40986000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr21:40982800-40986400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr21:40983200-40985600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr21:40983200-40987600	Active TSS	Brain Anterior Caudate	brain
6	chr21:40983400-40985200	Bivalent Enhancer	Fetal Brain Male	brain
7	chr21:40983400-40985600	Active TSS	Pancreas	Pancrea
8	chr21:40983400-40985800	Active TSS	Brain Hippocampus Middle	brain
9	chr21:40983400-40986200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:40983600-40984800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr21:40983600-40985200	Active TSS	Brain Substantia Nigra	brain
12	chr21:40983600-40985800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr21:40983600-40986000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr21:40983600-40986000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr21:40983600-40986200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr21:40983600-40986600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
17	chr21:40983800-40985200	Enhancers	Fetal Heart	heart
18	chr21:40983800-40985600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr21:40984000-40985200	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr21:40984000-40985200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
21	chr21:40984000-40985400	Active TSS	Rectal Smooth Muscle	rectum
22	chr21:40984000-40985600	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr21:40984000-40986200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr21:40984200-40984800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr21:40984200-40985200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr21:40984200-40985200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr21:40984200-40985200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
28	chr21:40984200-40985200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr21:40984200-40985200	Bivalent/Poised TSS	Fetal Brain Female	brain
30	chr21:40984200-40985600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr21:40984200-40985600	Active TSS	Colon Smooth Muscle	Colon
32	chr21:40984200-40985600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
33	chr21:40984200-40985600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr21:40984200-40985800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
35	chr21:40984200-40985800	Bivalent/Poised TSS	NHDF-Ad	bronchial
36	chr21:40984200-40986000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
37	chr21:40984200-40987400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr21:40984400-40984800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr21:40984400-40984800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr21:40984400-40985000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr21:40984400-40985000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr21:40984400-40985000	Bivalent/Poised TSS	Ovary	ovary
43	chr21:40984400-40985200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr21:40984400-40985200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr21:40984400-40985200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
46	chr21:40984400-40985200	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr21:40984400-40985200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
48	chr21:40984400-40985400	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr21:40984400-40985400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr21:40984400-40985400	Bivalent Enhancer	Lung	lung

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