Variant report

Variant	rs541759068
Chromosome Location	chr3:196296070-196296071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:144)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:144 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr3:196295079-196296388	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr3:196295912-196296363	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr3:196295110-196296220	A549	lung:	n/a	n/a
4	CTCF	chr3:196296020-196296170	AoAF	blood vessel:	n/a	n/a
5	HCFC1	chr3:196293701-196297089	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr3:196296003-196296121	MCF-7	breast:	n/a	n/a
7	CHD2	chr3:196296057-196296235	GM12878	blood:	n/a	n/a
8	TBP	chr3:196296062-196296262	K562	blood:	n/a	n/a
9	POLR2A	chr3:196295164-196296245	GM18526	blood:	n/a	n/a
10	CTCF	chr3:196295940-196296090	GM12868	blood:	n/a	n/a
11	POLR2A	chr3:196295930-196296281	GM12878	blood:	n/a	n/a
12	UBTF	chr3:196295088-196296545	K562	blood:	n/a	n/a
13	HA-E2F1	chr3:196295124-196296256	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr3:196295960-196296110	AG04449	skin:	n/a	n/a
15	E2F1	chr3:196295164-196296393	Hela-S3	cervix:	n/a	n/a
16	ELF1	chr3:196296017-196296249	K562	blood:	n/a	n/a
17	MYC	chr3:196295207-196296228	MCF-7	breast:	n/a	chr3:196295552-196295561
18	TFAP2A	chr3:196295294-196296457	Hela-S3	cervix:	n/a	chr3:196296181-196296192 chr3:196295431-196295442 chr3:196296182-196296190 chr3:196296182-196296190 chr3:196296182-196296190
19	SIN3A	chr3:196294917-196296502	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr3:196296000-196296150	GM12873	blood:	n/a	n/a
21	CTCF	chr3:196295960-196296110	NHEK	skin:	n/a	n/a
22	CTCF	chr3:196295960-196296110	HMEC	breast:	n/a	n/a
23	POLR2A	chr3:196294890-196296373	K562	blood:	n/a	n/a
24	POLR2A	chr3:196295103-196296381	ProgFib	skin:	n/a	n/a
25	THAP1	chr3:196295134-196296221	K562	blood:	n/a	chr3:196295539-196295563
26	CTCF	chr3:196296060-196296210	HMEC	breast:	n/a	n/a
27	MYC	chr3:196296029-196296167	K562	blood:	n/a	n/a
28	POLR2A	chr3:196294993-196296344	MCF-7	breast:	n/a	n/a
29	REST	chr3:196295934-196296358	ECC-1	luminal epithelium:	n/a	chr3:196296210-196296220
30	MAX	chr3:196294721-196296371	ECC-1	luminal epithelium:	n/a	chr3:196295552-196295561
31	POLR2A	chr3:196295111-196296209	HUVEC	blood vessel:	n/a	n/a
32	CTCF	chr3:196295980-196296130	GM12865	blood:	n/a	n/a
33	RFX5	chr3:196296045-196296337	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr3:196296020-196296170	GM12868	blood:	n/a	n/a
35	RUNX3	chr3:196295920-196296295	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:196295910-196296461	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr3:196296000-196296150	HEEpiC	esophagus:	n/a	n/a
38	POLR2A	chr3:196294962-196296221	MCF10A-Er-Src	breast:	n/a	n/a
39	MAX	chr3:196294888-196296302	HepG2	liver:	n/a	chr3:196295552-196295561
40	YY1	chr3:196294974-196296362	K562	blood:	n/a	chr3:196296193-196296204
41	MYC	chr3:196296024-196296200	MCF-7	breast:	n/a	n/a
42	MTA3	chr3:196295931-196296555	GM12878	blood:	n/a	n/a
43	CCNT2	chr3:196295171-196296288	K562	blood:	n/a	n/a
44	POLR2A	chr3:196295122-196296250	GM12892	blood:	n/a	n/a
45	E2F6	chr3:196294998-196296318	K562	blood:	n/a	chr3:196295393-196295404
46	POLR2A	chr3:196295929-196296227	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:196294714-196296360	GM12892	blood:	n/a	n/a
48	CTCF	chr3:196295980-196296130	SK-N-SH_RA	brain:	n/a	n/a
49	PAX5	chr3:196295938-196296202	GM12878	blood:	n/a	n/a
50	CTCF	chr3:196296000-196296128	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:196296032-196296082	HRE	kidney:	n/a
2	chr3:196296032-196296082	SKMC	muscle:	n/a
3	chr3:196296032-196296082	GM12891	blood:	n/a
4	chr3:196296032-196296082	U87	brain:	n/a
5	chr3:196296032-196296082	HUVEC	blood vessel:	n/a
6	chr3:196296032-196296082	AG09309	skin:	n/a
7	chr3:196296032-196296082	HRCEpiC	kidney:	n/a
8	chr3:196296032-196296082	BJ	skin:	n/a
9	chr3:196296032-196296082	NHBE	bronchial:	n/a
10	chr3:196296032-196296082	GM19239	blood:	n/a
11	chr3:196296032-196296082	Caco-2	colon:	n/a
12	chr3:196296032-196296082	RPTEC	kidney:	n/a
13	chr3:196296032-196296082	HAEpiC	amniotic membrane:	n/a
14	chr3:196296032-196296082	Hepatocyte	liver:	n/a
15	chr3:196296032-196296082	HRPEpiC	eye:	n/a
16	chr3:196296032-196296082	Jurkat	blood:	n/a
17	chr3:196296032-196296082	HIPEpiC	eye:	n/a
18	chr3:196296032-196296082	CMK	blood:	n/a
19	chr3:196296032-196296082	IMR90	lung:	fetal
20	chr3:196296032-196296082	HNPCEpiC	eye:	n/a
21	chr3:196296032-196296082	HPAEpiC	pulmonary alveolar:	n/a
22	chr3:196296032-196296082	HCT-116	colon:	n/a
23	chr3:196296032-196296082	PANC-1	pancreas:	n/a
24	chr3:196296032-196296082	HCM	heart:	n/a
25	chr3:196296032-196296082	SAEC	small airway:	n/a
26	chr3:196296032-196296082	BE2_C	brain:	n/a
27	chr3:196296032-196296082	HMEC	breast:	n/a
28	chr3:196296032-196296082	GM12878	blood:	n/a
29	chr3:196296032-196296082	MCF-7	breast:	n/a
30	chr3:196296032-196296082	AG04449	skin:	fetal
31	chr3:196296032-196296082	HL-60	blood:	n/a
32	chr3:196296032-196296082	MCF10A-Er-Src	breast:	n/a
33	chr3:196296032-196296082	HCF	heart:	n/a
34	chr3:196296032-196296082	SK-N-MC	brain:	n/a
35	chr3:196296032-196296082	NT2-D1	testis:	n/a
36	chr3:196296032-196296082	SK-N-SH	brain:	n/a
37	chr3:196296032-196296082	T-47D	breast:	n/a
38	chr3:196296032-196296082	GM12892	blood:	n/a
39	chr3:196296032-196296082	GM06990	blood:	n/a
40	chr3:196296032-196296082	A549	lung:	n/a
41	chr3:196296032-196296082	HCPEpiC	choroid plexus:	n/a
42	chr3:196296032-196296082	HepG2	liver:	n/a
43	chr3:196296032-196296082	AG10803	skin:	n/a
44	chr3:196296032-196296082	ProgFib	skin:	n/a
45	chr3:196296032-196296082	ECC-1	luminal epithelium:	n/a
46	chr3:196296032-196296082	AoSMC	blood vessel:	n/a
47	chr3:196296032-196296082	NB4	blood:	n/a
48	chr3:196296032-196296082	AG09319	gingival:	n/a
49	chr3:196296032-196296082	HEK293	kidney:	embryo
50	chr3:196296032-196296082	NH-A	brain:	n/a

(count:14 , 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	chr3:196228489..196231887-chr3:196292830..196296417,3	MCF-7	breast:
6	chr3:196294271..196297444-chr3:196668008..196671102,4	K562	blood:
7	chr3:196294935..196297677-chr3:196667748..196670021,2	MCF-7	breast:
8	chr3:196295234..196297248-chr3:196695881..196697586,3	MCF-7	breast:
9	chr3:196294586..196296980-chr3:196730003..196731682,2	MCF-7	breast:
10	chr3:196295485..196297090-chr3:196694773..196696786,2	MCF-7	breast:
11	chr3:196293733..196296360-chr3:196359092..196361282,2	MCF-7	breast:
12	chr3:196294356..196296088-chr3:196755433..196757925,2	K562	blood:
13	chr14:64804923..64805825-chr3:196295231..196296081,2	Hela-S3	cervix:
14	chr3:196228351..196232071-chr3:196294107..196297178,4	MCF-7	breast:

No data

Variant related genes	Relation type
WDR53	TF binding region
WDR53	CpG island
ENSG00000228109	Chromatin interaction
ENSG00000119227	Chromatin interaction
ENSG00000214770	Chromatin interaction
ENSG00000232065	Chromatin interaction
ENSG00000270170	Chromatin interaction
ENSG00000213358	Chromatin interaction
ENSG00000114503	Chromatin interaction
ENSG00000163961	Chromatin interaction
ENSG00000163975	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	chr3:196294800-196296200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:196294800-196296200	Active TSS	Brain Substantia Nigra	brain
25	chr3:196294800-196296200	Active TSS	Fetal Muscle Trunk	muscle
26	chr3:196294800-196296200	Active TSS	Thymus	Thymus
27	chr3:196294800-196296200	Active TSS	NH-A	brain
28	chr3:196294800-196296400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr3:196294800-196296400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:196294800-196296400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:196294800-196296400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:196294800-196296400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:196294800-196296400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:196294800-196296400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr3:196294800-196296400	Active TSS	Brain Hippocampus Middle	brain
36	chr3:196294800-196296400	Active TSS	Fetal Intestine Small	intestine
37	chr3:196294800-196296400	Active TSS	Gastric	stomach
38	chr3:196294800-196296400	Active TSS	Pancreas	Pancrea
39	chr3:196294800-196296400	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr3:196294800-196296600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr3:196294800-196296600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:196294800-196296600	Active TSS	Aorta	Aorta
43	chr3:196294800-196296600	Active TSS	Fetal Kidney	kidney
44	chr3:196294800-196296600	Active TSS	Ovary	ovary
45	chr3:196294800-196296600	Active TSS	Right Atrium	heart
46	chr3:196294800-196296600	Active TSS	HMEC	breast
47	chr3:196294800-196296600	Active TSS	NHDF-Ad	bronchial
48	chr3:196294800-196296800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:196294800-196296800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:196294800-196296800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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