Variant report

Variant	rs62219499
Chromosome Location	chr21:17566523-17566524
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr21:17566033-17566938	HEK293	kidney:	n/a	n/a
2	RCOR1	chr21:17566232-17567495	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr21:17566238-17566984	A549	lung:	n/a	n/a
4	TAF1	chr21:17566281-17566966	Hela-S3	cervix:	n/a	n/a
5	TFAP2A	chr21:17566273-17566800	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr21:17566214-17566950	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr21:17566085-17567036	GM12878	blood:	n/a	n/a
8	SP1	chr21:17566242-17566740	A549	lung:	n/a	n/a
9	POLR2A	chr21:17566216-17568279	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr21:17566231-17566951	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr21:17566287-17566928	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr21:17566348-17567613	Hela-S3	cervix:	n/a	n/a
13	EP300	chr21:17566241-17567002	ECC-1	luminal epithelium:	n/a	chr21:17566542-17566551
14	RAD21	chr21:17566331-17567531	Hela-S3	cervix:	n/a	n/a
15	TCF12	chr21:17566254-17566920	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr21:17565985-17569122	Hela-S3	cervix:	n/a	n/a
17	EP300	chr21:17566205-17566758	A549	lung:	n/a	chr21:17566542-17566551
18	POLR2A	chr21:17566207-17567682	HUVEC	blood vessel:	n/a	n/a
19	SP1	chr21:17566243-17566917	A549	lung:	n/a	n/a
20	POLR2A	chr21:17566511-17566654	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr21:17566206-17568768	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA3	chr21:17566128-17566809	A549	lung:	n/a	n/a
23	YY1	chr21:17566272-17566693	ECC-1	luminal epithelium:	n/a	n/a
24	RUNX3	chr21:17566208-17567332	GM12878	blood:	n/a	n/a
25	TEAD4	chr21:17566255-17566797	ECC-1	luminal epithelium:	n/a	n/a
26	ESR1	chr21:17566239-17566679	ECC-1	luminal epithelium:	n/a	n/a
27	KAP1	chr21:17566284-17567437	U2OS	brain:	n/a	n/a
28	RAD21	chr21:17566338-17567110	ECC-1	luminal epithelium:	n/a	n/a
29	CHD2	chr21:17566312-17567001	Hela-S3	cervix:	n/a	n/a
30	TAF1	chr21:17566385-17566635	Hela-S3	cervix:	n/a	n/a
31	E2F4	chr21:17566483-17566682	MCF10A-Er-Src	breast:	n/a	n/a
32	YY1	chr21:17566338-17566567	GM12892	blood:	n/a	n/a
33	MXI1	chr21:17566336-17567452	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr21:17566251-17567045	U87	brain:	n/a	n/a
35	POLR2A	chr21:17566219-17566963	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr21:17566247-17566964	HUVEC	blood vessel:	n/a	n/a
37	TBP	chr21:17566226-17569501	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr21:17566282-17567207	U87	brain:	n/a	n/a
39	TFAP2C	chr21:17566104-17566730	Hela-S3	cervix:	n/a	n/a
40	ESR1	chr21:17566192-17566608	ECC-1	luminal epithelium:	n/a	n/a
41	KAP1	chr21:17566231-17567460	HEK293	kidney:	n/a	n/a
42	SP1	chr21:17566270-17566734	H1-hESC	embryonic stem cell:	n/a	n/a
43	SMC3	chr21:17566287-17567523	Hela-S3	cervix:	n/a	n/a
44	BRCA1	chr21:17566254-17567494	Hela-S3	cervix:	n/a	n/a
45	GATA2	chr21:17566359-17567500	HUVEC	blood vessel:	n/a	chr21:17567336-17567343
46	MAX	chr21:17566307-17566959	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr21:17566257-17566958	Hela-S3	cervix:	n/a	n/a
48	SIN3AK20	chr21:17566275-17566627	PFSK-1	brain:	n/a	n/a
49	YY1	chr21:17566271-17566556	H1-hESC	embryonic stem cell:	n/a	n/a
50	TEAD4	chr21:17566186-17566809	ECC-1	luminal epithelium:	n/a	n/a

No data

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

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

No data

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

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12106318	0.80[EUR][1000 genomes]
rs59897117	0.83[EUR][1000 genomes]
rs62219500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62219532	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62219534	0.80[EUR][1000 genomes]
rs62221870	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73890704	0.83[EUR][1000 genomes]
rs8132985	0.80[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:84 , 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	chr21:17559600-17566600	Weak transcription	Placenta	Placenta
3	chr21:17563600-17567200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr21:17565200-17566600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr21:17565400-17570000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr21:17565600-17566600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr21:17565600-17566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr21:17565600-17566600	Weak transcription	Thymus	Thymus
9	chr21:17565800-17566600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr21:17565800-17566800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr21:17566000-17566600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr21:17566000-17568000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr21:17566200-17566600	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr21:17566200-17566600	Flanking Active TSS	Fetal Muscle Leg	muscle
15	chr21:17566200-17566600	Flanking Active TSS	Osteobl	bone
16	chr21:17566200-17566800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr21:17566200-17566800	Flanking Active TSS	HUVEC	blood vessel
18	chr21:17566200-17567400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr21:17566200-17567600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr21:17566200-17568400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr21:17566200-17569200	Active TSS	Fetal Muscle Trunk	muscle
22	chr21:17566200-17569400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr21:17566200-17569400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr21:17566200-17569400	Active TSS	Brain Hippocampus Middle	brain
25	chr21:17566200-17569600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr21:17566200-17569600	Active TSS	Ovary	ovary
27	chr21:17566200-17569600	Active TSS	Psoas Muscle	Psoas
28	chr21:17566200-17569600	Active TSS	GM12878-XiMat	blood
29	chr21:17566200-17569800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr21:17566200-17569800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr21:17566200-17569800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr21:17566200-17569800	Active TSS	Brain Germinal Matrix	brain
33	chr21:17566200-17570000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr21:17566200-17570000	Active TSS	Right Atrium	heart
35	chr21:17566400-17566600	Enhancers	Primary B cells from cord blood	blood
36	chr21:17566400-17566600	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr21:17566400-17566600	Flanking Active TSS	Brain Angular Gyrus	brain
38	chr21:17566400-17566600	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr21:17566400-17566600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr21:17566400-17566600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr21:17566400-17566600	Enhancers	Fetal Brain Male	brain
42	chr21:17566400-17566600	Enhancers	Fetal Heart	heart
43	chr21:17566400-17566600	Flanking Active TSS	Fetal Kidney	kidney
44	chr21:17566400-17566600	Flanking Active TSS	HSMM	muscle
45	chr21:17566400-17566800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr21:17566400-17566800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr21:17566400-17566800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr21:17566400-17566800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr21:17566400-17566800	Enhancers	Duodenum Mucosa	Duodenum
50	chr21:17566400-17566800	Enhancers	Fetal Brain Female	brain

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