Variant report

Variant	rs549514287
Chromosome Location	chr3:196295603-196295604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:505)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:505 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:196295187-196295894	K562	blood:	n/a	n/a
2	POLR2A	chr3:196294841-196295901	Hela-S3	cervix:	n/a	n/a
3	BHLHE40	chr3:196295162-196295671	K562	blood:	n/a	chr3:196295647-196295663
4	CREB1	chr3:196294989-196295767	ECC-1	luminal epithelium:	n/a	n/a
5	SIX5	chr3:196295136-196295702	A549	lung:	n/a	n/a
6	SIN3AK20	chr3:196295079-196296388	PANC-1	pancreas:	n/a	n/a
7	HEY1	chr3:196295054-196295926	HepG2	liver:	n/a	chr3:196295565-196295580
8	MAX	chr3:196295096-196295804	A549	lung:	n/a	chr3:196295552-196295561
9	CHD2	chr3:196295200-196295778	Hela-S3	cervix:	n/a	n/a
10	SP4	chr3:196294987-196295620	H1-hESC	embryonic stem cell:	n/a	chr3:196295402-196295413
11	BRCA1	chr3:196295296-196295633	H1-hESC	embryonic stem cell:	n/a	n/a
12	ETS1	chr3:196295184-196295794	GM12878	blood:	n/a	chr3:196295391-196295402
13	IRF4	chr3:196295204-196295717	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:196295110-196296220	A549	lung:	n/a	n/a
15	ATF1	chr3:196295005-196295685	K562	blood:	n/a	n/a
16	YY1	chr3:196295204-196295806	A549	lung:	n/a	n/a
17	ZEB1	chr3:196295214-196295758	GM12878	blood:	n/a	n/a
18	CHD2	chr3:196295214-196295653	HepG2	liver:	n/a	n/a
19	MAZ	chr3:196295132-196295775	K562	blood:	n/a	chr3:196295552-196295561
20	HCFC1	chr3:196293701-196297089	Hela-S3	cervix:	n/a	n/a
21	SIN3AK20	chr3:196295044-196295901	SK-N-SH	brain:	n/a	n/a
22	SRF	chr3:196295087-196295855	ECC-1	luminal epithelium:	n/a	n/a
23	RCOR1	chr3:196295169-196295740	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:196294913-196295833	GM12878	blood:	n/a	n/a
25	CTCF	chr3:196295580-196295730	GM12868	blood:	n/a	n/a
26	MAX	chr3:196295251-196295738	K562	blood:	n/a	chr3:196295552-196295561
27	FOXM1	chr3:196295064-196295739	GM12878	blood:	n/a	n/a
28	E2F6	chr3:196294950-196295806	H1-hESC	embryonic stem cell:	n/a	chr3:196295393-196295404
29	MAX	chr3:196295008-196295936	A549	lung:	n/a	chr3:196295552-196295561
30	SRF	chr3:196295023-196295807	MCF-7	breast:	n/a	n/a
31	POLR2A	chr3:196295164-196296245	GM18526	blood:	n/a	n/a
32	POLR2A	chr3:196295179-196295718	HepG2	liver:	n/a	n/a
33	POU2F2	chr3:196295461-196295632	GM12878	blood:	n/a	n/a
34	MAX	chr3:196295039-196295873	SK-N-SH	brain:	n/a	chr3:196295552-196295561
35	ELF1	chr3:196295234-196295771	HepG2	liver:	n/a	n/a
36	GABPA	chr3:196295180-196295695	Hela-S3	cervix:	n/a	chr3:196295608-196295617
37	GTF2B	chr3:196295206-196295677	K562	blood:	n/a	n/a
38	POLR2A	chr3:196295127-196295845	SK-N-MC	brain:	n/a	n/a
39	EP300	chr3:196294969-196295851	T-47D	breast:	n/a	chr3:196295608-196295617 chr3:196295610-196295626
40	UBTF	chr3:196295088-196296545	K562	blood:	n/a	n/a
41	CHD1	chr3:196295168-196295732	GM12878	blood:	n/a	n/a
42	CHD2	chr3:196295293-196295619	K562	blood:	n/a	n/a
43	REST	chr3:196295206-196295736	PANC-1	pancreas:	n/a	chr3:196295574-196295587
44	POLR2A	chr3:196295251-196295765	HepG2	liver:	n/a	n/a
45	HA-E2F1	chr3:196295124-196296256	Hela-S3	cervix:	n/a	n/a
46	MAX	chr3:196295159-196295782	NB4	blood:	n/a	chr3:196295552-196295561
47	SP1	chr3:196295127-196295832	A549	lung:	n/a	chr3:196295402-196295413
48	REST	chr3:196295186-196295744	HepG2	liver:	n/a	chr3:196295574-196295587
49	SP1	chr3:196295251-196295626	GM12878	blood:	n/a	chr3:196295402-196295413
50	SP1	chr3:196295167-196295621	H1-hESC	embryonic stem cell:	n/a	chr3:196295402-196295413

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196294811..196297703-chr3:196694216..196696736,3	K562	blood:
2	chr3:196292428..196296416-chr3:196668494..196671676,5	MCF-7	breast:
3	chr3:196253926..196256027-chr3:196295277..196297106,2	K562	blood:
4	chr3:196294271..196297444-chr3:196668008..196671102,3	K562	blood:
5	chr3:196294148..196296034-chr6:26157528..26159567,2	MCF-7	breast:
6	chr3:196228489..196231887-chr3:196292830..196296417,3	MCF-7	breast:
7	chr17:73775423..73776072-chr3:196295009..196295935,2	Hela-S3	cervix:
8	chr3:196294271..196297444-chr3:196668008..196671102,4	K562	blood:
9	chr3:196294935..196297677-chr3:196667748..196670021,2	MCF-7	breast:
10	chr3:196295234..196297248-chr3:196695881..196697586,3	MCF-7	breast:
11	chr3:196294586..196296980-chr3:196730003..196731682,2	MCF-7	breast:
12	chr3:196295485..196297090-chr3:196694773..196696786,2	MCF-7	breast:
13	chr3:196293710..196295856-chr3:196756425..196758030,2	K562	blood:
14	chr3:196293733..196296360-chr3:196359092..196361282,2	MCF-7	breast:
15	chr3:196294356..196296088-chr3:196755433..196757925,2	K562	blood:
16	chr14:64804923..64805825-chr3:196295231..196296081,2	Hela-S3	cervix:
17	chr3:196228351..196232071-chr3:196294107..196297178,4	MCF-7	breast:

No data

Variant related genes	Relation type
WDR53	TF binding region
ENSG00000228109	Chromatin interaction
ENSG00000270170	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000163975	Chromatin interaction
ENSG00000119227	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000214770	Chromatin interaction
ENSG00000114503	Chromatin interaction
ENSG00000213358	Chromatin interaction
ENSG00000232065	Chromatin interaction
ENSG00000163961	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers 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 miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	esv3347483	chr3:196294955-196297053	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 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	chr3:196294000-196296400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:196294200-196296200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:196294200-196296600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:196294200-196296600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr3:196294200-196296800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr3:196294200-196297000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:196294400-196296600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:196294400-196296800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:196294400-196296800	Active TSS	Right Ventricle	heart
10	chr3:196294400-196296800	Active TSS	HSMM	muscle
11	chr3:196294400-196297000	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:196294400-196297000	Active TSS	A549	lung
13	chr3:196294400-196297200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:196294600-196296200	Active TSS	HSMMtube	muscle
15	chr3:196294600-196296400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:196294600-196296400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:196294600-196296400	Active TSS	K562	blood
18	chr3:196294600-196296600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:196294600-196296600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:196294600-196296600	Active TSS	Placenta Amnion	Placenta Amnion
21	chr3:196294600-196296800	Active TSS	Small Intestine	intestine
22	chr3:196294600-196297000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:196294800-196296000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:196294800-196296000	Active TSS	Brain Germinal Matrix	brain
25	chr3:196294800-196296000	Active TSS	Lung	lung
26	chr3:196294800-196296200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:196294800-196296200	Active TSS	Brain Substantia Nigra	brain
28	chr3:196294800-196296200	Active TSS	Fetal Muscle Trunk	muscle
29	chr3:196294800-196296200	Active TSS	Thymus	Thymus
30	chr3:196294800-196296200	Active TSS	NH-A	brain
31	chr3:196294800-196296400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr3:196294800-196296400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:196294800-196296400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:196294800-196296400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:196294800-196296400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:196294800-196296400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:196294800-196296400	Active TSS	Muscle Satellite Cultured Cells	--
38	chr3:196294800-196296400	Active TSS	Brain Hippocampus Middle	brain
39	chr3:196294800-196296400	Active TSS	Fetal Intestine Small	intestine
40	chr3:196294800-196296400	Active TSS	Gastric	stomach
41	chr3:196294800-196296400	Active TSS	Pancreas	Pancrea
42	chr3:196294800-196296400	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr3:196294800-196296600	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr3:196294800-196296600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:196294800-196296600	Active TSS	Aorta	Aorta
46	chr3:196294800-196296600	Active TSS	Fetal Kidney	kidney
47	chr3:196294800-196296600	Active TSS	Ovary	ovary
48	chr3:196294800-196296600	Active TSS	Right Atrium	heart
49	chr3:196294800-196296600	Active TSS	HMEC	breast
50	chr3:196294800-196296600	Active TSS	NHDF-Ad	bronchial

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