Variant report

Variant	rs16994440
Chromosome Location	chr21:17566736-17566737
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:90)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:90 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr21:17566717-17566930	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr21:17566673-17566942	HepG2	liver:	n/a	n/a
3	RUNX3	chr21:17566584-17567238	GM12878	blood:	n/a	n/a
4	TCF7L2	chr21:17566033-17566938	HEK293	kidney:	n/a	n/a
5	SIN3AK20	chr21:17566732-17566912	PFSK-1	brain:	n/a	n/a
6	RCOR1	chr21:17566232-17567495	Hela-S3	cervix:	n/a	n/a
7	TCF12	chr21:17566238-17566984	A549	lung:	n/a	n/a
8	CTCF	chr21:17566720-17566870	HRPEpiC	eye:	n/a	n/a
9	TAF1	chr21:17566281-17566966	Hela-S3	cervix:	n/a	n/a
10	TFAP2A	chr21:17566273-17566800	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr21:17566214-17566950	ECC-1	luminal epithelium:	n/a	n/a
12	NFIC	chr21:17566085-17567036	GM12878	blood:	n/a	n/a
13	RAD21	chr21:17566703-17566924	HepG2	liver:	n/a	n/a
14	SP1	chr21:17566242-17566740	A549	lung:	n/a	n/a
15	CTCF	chr21:17566730-17566912	GM12878	blood:	n/a	n/a
16	CTCF	chr21:17566720-17566870	AG04450	lung:	n/a	n/a
17	POLR2A	chr21:17566216-17568279	MCF10A-Er-Src	breast:	n/a	n/a
18	RAD21	chr21:17566712-17566947	HepG2	liver:	n/a	n/a
19	RAD21	chr21:17566603-17567007	A549	lung:	n/a	n/a
20	CTCF	chr21:17566636-17567011	GM12878	blood:	n/a	n/a
21	CTCF	chr21:17566698-17566897	HepG2	liver:	n/a	n/a
22	POLR2A	chr21:17566231-17566951	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr21:17566287-17566928	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr21:17566348-17567613	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr21:17566582-17566966	H1-hESC	embryonic stem cell:	n/a	n/a
26	EP300	chr21:17566241-17567002	ECC-1	luminal epithelium:	n/a	chr21:17566542-17566551
27	RAD21	chr21:17566331-17567531	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr21:17566700-17566850	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr21:17566720-17566870	Caco-2	colon:	n/a	n/a
30	TCF12	chr21:17566254-17566920	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr21:17566720-17566870	AoAF	blood vessel:	n/a	n/a
32	POLR2A	chr21:17565985-17569122	Hela-S3	cervix:	n/a	n/a
33	EP300	chr21:17566205-17566758	A549	lung:	n/a	chr21:17566542-17566551
34	POLR2A	chr21:17566207-17567682	HUVEC	blood vessel:	n/a	n/a
35	SP1	chr21:17566243-17566917	A549	lung:	n/a	n/a
36	CTCF	chr21:17566720-17566870	HCM	heart:	n/a	n/a
37	CTCF	chr21:17566660-17566810	HFF-Myc	foreskin:	n/a	n/a
38	CTCF	chr21:17566736-17566943	A549	lung:	n/a	n/a
39	RAD21	chr21:17566616-17567066	A549	lung:	n/a	n/a
40	RAD21	chr21:17566735-17566931	SK-N-SH_RA	brain:	n/a	n/a
41	CTCF	chr21:17566720-17566870	HRE	kidney:	n/a	n/a
42	POLR2A	chr21:17566206-17568768	MCF10A-Er-Src	breast:	n/a	n/a
43	GATA3	chr21:17566128-17566809	A549	lung:	n/a	n/a
44	RUNX3	chr21:17566208-17567332	GM12878	blood:	n/a	n/a
45	RAD21	chr21:17566706-17566940	A549	lung:	n/a	n/a
46	TEAD4	chr21:17566255-17566797	ECC-1	luminal epithelium:	n/a	n/a
47	BCLAF1	chr21:17566541-17567013	GM12878	blood:	n/a	n/a
48	KAP1	chr21:17566284-17567437	U2OS	brain:	n/a	n/a
49	RAD21	chr21:17566338-17567110	ECC-1	luminal epithelium:	n/a	n/a
50	CHD2	chr21:17566312-17567001	Hela-S3	cervix:	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:3 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1492961	1.00[AMR][1000 genomes]
rs16994415	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16994421	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16994425	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16994427	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16994429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16994433	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16994610	1.00[AMR][1000 genomes]
rs16994646	1.00[AMR][1000 genomes]
rs239081	1.00[AMR][1000 genomes]
rs41417245	1.00[AMR][1000 genomes]
rs8127337	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8127343	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8129316	1.00[AMR][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:95 , 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	chr21:17565800-17566800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr21:17566000-17568000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr21:17566200-17566800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr21:17566200-17566800	Flanking Active TSS	HUVEC	blood vessel
8	chr21:17566200-17567400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr21:17566200-17567600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr21:17566200-17568400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:17566200-17569200	Active TSS	Fetal Muscle Trunk	muscle
12	chr21:17566200-17569400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr21:17566200-17569400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr21:17566200-17569400	Active TSS	Brain Hippocampus Middle	brain
15	chr21:17566200-17569600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr21:17566200-17569600	Active TSS	Ovary	ovary
17	chr21:17566200-17569600	Active TSS	Psoas Muscle	Psoas
18	chr21:17566200-17569600	Active TSS	GM12878-XiMat	blood
19	chr21:17566200-17569800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr21:17566200-17569800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr21:17566200-17569800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr21:17566200-17569800	Active TSS	Brain Germinal Matrix	brain
23	chr21:17566200-17570000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:17566200-17570000	Active TSS	Right Atrium	heart
25	chr21:17566400-17566800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr21:17566400-17566800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr21:17566400-17566800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr21:17566400-17566800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr21:17566400-17566800	Enhancers	Duodenum Mucosa	Duodenum
30	chr21:17566400-17566800	Enhancers	Fetal Brain Female	brain
31	chr21:17566400-17566800	Flanking Active TSS	Dnd41	blood
32	chr21:17566400-17567000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr21:17566400-17567200	Flanking Active TSS	NH-A	brain
34	chr21:17566400-17567400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr21:17566400-17567400	Enhancers	Primary B cells from peripheral blood	blood
36	chr21:17566400-17567600	Active TSS	Left Ventricle	heart
37	chr21:17566400-17567600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr21:17566400-17567800	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr21:17566400-17568000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr21:17566400-17568000	Active TSS	Fetal Intestine Large	intestine
41	chr21:17566400-17568000	Flanking Active TSS	Fetal Lung	lung
42	chr21:17566400-17568200	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr21:17566400-17568600	Active TSS	Fetal Thymus	thymus
44	chr21:17566400-17568800	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr21:17566400-17569000	Active TSS	Fetal Intestine Small	intestine
46	chr21:17566400-17569200	Active TSS	Liver	Liver
47	chr21:17566400-17569400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr21:17566400-17569400	Active TSS	Brain Cingulate Gyrus	brain
49	chr21:17566400-17569400	Active TSS	A549	lung
50	chr21:17566400-17569600	Active TSS	Aorta	Aorta

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