Variant report

Variant	rs62219500
Chromosome Location	chr21:17566807-17566808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:156)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:156 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:17566760-17566910	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr21:17566717-17566930	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr21:17566673-17566942	HepG2	liver:	n/a	n/a
4	RUNX3	chr21:17566584-17567238	GM12878	blood:	n/a	n/a
5	TCF7L2	chr21:17566033-17566938	HEK293	kidney:	n/a	n/a
6	SIN3AK20	chr21:17566732-17566912	PFSK-1	brain:	n/a	n/a
7	RCOR1	chr21:17566232-17567495	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr21:17566780-17566930	HPF	lung:	n/a	n/a
9	TCF12	chr21:17566238-17566984	A549	lung:	n/a	n/a
10	CTCF	chr21:17566720-17566870	HRPEpiC	eye:	n/a	n/a
11	TAF1	chr21:17566281-17566966	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr21:17566800-17566950	HCPEpiC	choroid plexus:	n/a	n/a
13	POLR2A	chr21:17566214-17566950	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr21:17566085-17567036	GM12878	blood:	n/a	n/a
15	CTCF	chr21:17566800-17566950	HFF-Myc	foreskin:	n/a	n/a
16	RAD21	chr21:17566703-17566924	HepG2	liver:	n/a	n/a
17	CTCF	chr21:17566730-17566912	GM12878	blood:	n/a	n/a
18	CTCF	chr21:17566720-17566870	AG04450	lung:	n/a	n/a
19	POLR2A	chr21:17566216-17568279	MCF10A-Er-Src	breast:	n/a	n/a
20	RAD21	chr21:17566712-17566947	HepG2	liver:	n/a	n/a
21	CTCF	chr21:17566760-17566910	HBMEC	blood vessel:	n/a	n/a
22	RAD21	chr21:17566603-17567007	A549	lung:	n/a	n/a
23	CTCF	chr21:17566780-17566930	AG04449	skin:	n/a	n/a
24	CTCF	chr21:17566791-17566896	GM19238	blood:	n/a	n/a
25	CTCF	chr21:17566740-17566890	BE2_C	brain:	n/a	n/a
26	CTCF	chr21:17566760-17566910	GM12878	blood:	n/a	n/a
27	CTCF	chr21:17566636-17567011	GM12878	blood:	n/a	n/a
28	CTCF	chr21:17566698-17566897	HepG2	liver:	n/a	n/a
29	POLR2A	chr21:17566231-17566951	PFSK-1	brain:	n/a	n/a
30	CTCF	chr21:17566777-17566924	MCF-7	breast:	n/a	n/a
31	POLR2A	chr21:17566287-17566928	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr21:17566348-17567613	Hela-S3	cervix:	n/a	n/a
33	RAD21	chr21:17566582-17566966	H1-hESC	embryonic stem cell:	n/a	n/a
34	EP300	chr21:17566241-17567002	ECC-1	luminal epithelium:	n/a	chr21:17566542-17566551
35	RAD21	chr21:17566331-17567531	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr21:17566780-17566930	AG10803	skin:	n/a	n/a
37	CTCF	chr21:17566700-17566850	HUVEC	blood vessel:	n/a	n/a
38	CTCF	chr21:17566720-17566870	Caco-2	colon:	n/a	n/a
39	CTCF	chr21:17566780-17566930	HMEC	breast:	n/a	n/a
40	TCF12	chr21:17566254-17566920	ECC-1	luminal epithelium:	n/a	n/a
41	CTCF	chr21:17566720-17566870	AoAF	blood vessel:	n/a	n/a
42	CTCF	chr21:17566760-17566910	NHLF	lung:	n/a	n/a
43	POLR2A	chr21:17565985-17569122	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr21:17566207-17567682	HUVEC	blood vessel:	n/a	n/a
45	SP1	chr21:17566243-17566917	A549	lung:	n/a	n/a
46	CTCF	chr21:17566780-17566930	HVMF	connective:	n/a	n/a
47	CTCF	chr21:17566720-17566870	HCM	heart:	n/a	n/a
48	CTCF	chr21:17566780-17566930	BJ	skin:	n/a	n/a
49	CTCF	chr21:17566761-17566932	LNCaP	prostate:	n/a	n/a
50	CTCF	chr21:17566780-17566930	HEK293	kidney:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:77751904..77752690-chr21:17566657..17567443,2	Hela-S3	cervix:
2	chr16:89989331..89990190-chr21:17566356..17566935,2	Hela-S3	cervix:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP25-2	chr21:17566788-17566953	ENSG00000215386
2	lnc-USP25-2	chr21:17566715-17566953	ENSG00000215386.6
3	lnc-USP25-2	chr21:17566699-17566953	NONHSAT081228
4	lnc-USP25-2	chr21:17566699-17566953	ENSG00000215386

No data

Variant related genes	Relation type
LINC00478	TF binding region
ENSG00000173894	Chromatin interaction
ENSG00000258947	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12106318	0.83[EUR][1000 genomes]
rs12106447	0.81[EUR][1000 genomes]
rs2823644	0.81[EUR][1000 genomes]
rs2823648	0.81[EUR][1000 genomes]
rs55847255	0.81[EUR][1000 genomes]
rs59897117	0.85[EUR][1000 genomes]
rs62219499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62219532	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62219534	0.83[EUR][1000 genomes]
rs62221870	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73890704	0.85[EUR][1000 genomes]
rs8132985	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066951	chr21:17458978-17603160	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv544381	chr21:17458978-17603160	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1065028	chr21:17522588-17572535	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv432145	chr21:17559229-17628529	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv834051	chr21:17564843-17721764	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17559000-17571200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:17563600-17567200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr21:17565400-17570000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr21:17566000-17568000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr21:17566200-17567400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr21:17566200-17567600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr21:17566200-17568400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr21:17566200-17569200	Active TSS	Fetal Muscle Trunk	muscle
9	chr21:17566200-17569400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr21:17566200-17569400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr21:17566200-17569400	Active TSS	Brain Hippocampus Middle	brain
12	chr21:17566200-17569600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr21:17566200-17569600	Active TSS	Ovary	ovary
14	chr21:17566200-17569600	Active TSS	Psoas Muscle	Psoas
15	chr21:17566200-17569600	Active TSS	GM12878-XiMat	blood
16	chr21:17566200-17569800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr21:17566200-17569800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr21:17566200-17569800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr21:17566200-17569800	Active TSS	Brain Germinal Matrix	brain
20	chr21:17566200-17570000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr21:17566200-17570000	Active TSS	Right Atrium	heart
22	chr21:17566400-17567000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr21:17566400-17567200	Flanking Active TSS	NH-A	brain
24	chr21:17566400-17567400	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr21:17566400-17567400	Enhancers	Primary B cells from peripheral blood	blood
26	chr21:17566400-17567600	Active TSS	Left Ventricle	heart
27	chr21:17566400-17567600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr21:17566400-17567800	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr21:17566400-17568000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr21:17566400-17568000	Active TSS	Fetal Intestine Large	intestine
31	chr21:17566400-17568000	Flanking Active TSS	Fetal Lung	lung
32	chr21:17566400-17568200	Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr21:17566400-17568600	Active TSS	Fetal Thymus	thymus
34	chr21:17566400-17568800	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr21:17566400-17569000	Active TSS	Fetal Intestine Small	intestine
36	chr21:17566400-17569200	Active TSS	Liver	Liver
37	chr21:17566400-17569400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr21:17566400-17569400	Active TSS	Brain Cingulate Gyrus	brain
39	chr21:17566400-17569400	Active TSS	A549	lung
40	chr21:17566400-17569600	Active TSS	Aorta	Aorta
41	chr21:17566400-17569600	Active TSS	Fetal Stomach	stomach
42	chr21:17566400-17569600	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr21:17566400-17569600	Active TSS	Hela-S3	cervix
44	chr21:17566400-17569600	Active TSS	HSMMtube	muscle
45	chr21:17566400-17569800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr21:17566400-17569800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr21:17566400-17569800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr21:17566400-17569800	Active TSS	Colon Smooth Muscle	Colon
49	chr21:17566400-17569800	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr21:17566400-17569800	Active TSS	Skeletal Muscle Male	skeletal muscle

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