Variant report

Variant	rs4687566
Chromosome Location	chr3:51572169-51572170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr3:51572151-51572897	HEK293	kidney:	n/a	n/a
2	BHLHE40	chr3:51572085-51573094	GM12878	blood:	n/a	chr3:51572904-51572920
3	MAZ	chr3:51571979-51574231	IMR90	lung:	n/a	n/a
4	RELA	chr3:51572063-51572938	GM18951	blood:	n/a	n/a
5	MAX	chr3:51571893-51572216	K562	blood:	n/a	n/a
6	SMARCC1	chr3:51572092-51573853	Hela-S3	cervix:	n/a	chr3:51573789-51573798 chr3:51573631-51573640
7	MAX	chr3:51572001-51572333	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr3:51571928-51573012	HCT-116	colon:	n/a	n/a
9	MXI1	chr3:51571741-51574162	SK-N-SH	brain:	n/a	n/a
10	RUNX3	chr3:51572001-51573009	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:51572049-51573235	K562	blood:	n/a	n/a
12	KAP1	chr3:51572105-51572715	U2OS	brain:	n/a	n/a
13	MAX	chr3:51571957-51572965	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr3:51572126-51573119	PBDE	blood:	n/a	n/a
15	MAX	chr3:51572041-51573061	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr3:51572099-51573090	GM15510	blood:	n/a	n/a
17	MAX	chr3:51572042-51572893	NB4	blood:	n/a	n/a
18	POLR2A	chr3:51572007-51573747	GM18505	blood:	n/a	n/a
19	CHD1	chr3:51571910-51574678	IMR90	lung:	n/a	n/a
20	POLR2A	chr3:51572091-51573144	GM12892	blood:	n/a	n/a
21	E2F6	chr3:51571978-51572999	K562	blood:	n/a	chr3:51572745-51572755
22	PML	chr3:51572120-51573065	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:51571955-51574159	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr3:51572085-51572935	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr3:51572084-51573066	GM12891	blood:	n/a	n/a
26	MAX	chr3:51572162-51573218	GM12878	blood:	n/a	n/a
27	MTA3	chr3:51572018-51572879	GM12878	blood:	n/a	n/a
28	RCOR1	chr3:51572114-51572973	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:51572128-51573082	H1-neurons	neurons:	n/a	n/a
30	WRNIP1	chr3:51572067-51572792	GM12878	blood:	n/a	n/a
31	HCFC1	chr3:51572081-51573297	Hela-S3	cervix:	n/a	n/a
32	NRF1	chr3:51572074-51572892	GM12878	blood:	n/a	chr3:51572690-51572699
33	POLR2A	chr3:51572019-51573319	Raji	blood:	n/a	n/a
34	CTCF	chr3:51572140-51572290	HA-sp	spinal cord:	n/a	n/a
35	POLR2A	chr3:51572044-51573720	Hela-S3	cervix:	n/a	n/a
36	MXI1	chr3:51572169-51572258	H1-hESC	embryonic stem cell:	n/a	n/a
37	MYC	chr3:51572028-51572907	NB4	blood:	n/a	n/a
38	MYC	chr3:51572068-51572265	MCF10A-Er-Src	breast:	n/a	n/a
39	MXI1	chr3:51571966-51574484	IMR90	lung:	n/a	n/a
40	POLR2A	chr3:51571989-51573029	H1-neurons	neurons:	n/a	n/a
41	MXI1	chr3:51571993-51573032	GM12878	blood:	n/a	n/a
42	TAF1	chr3:51571937-51573709	H1-hESC	embryonic stem cell:	n/a	n/a
43	SIN3A	chr3:51572108-51573681	H1-hESC	embryonic stem cell:	n/a	n/a
44	STAT5A	chr3:51571959-51572922	GM12878	blood:	n/a	chr3:51572586-51572594 chr3:51572692-51572704
45	REST	chr3:51571838-51573230	H1-neurons	neurons:	n/a	chr3:51572650-51572663

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51533211..51536812-chr3:51571944..51573713,3	MCF-7	breast:
2	chr3:51428771..51431051-chr3:51571775..51574665,3	K562	blood:
3	chr3:51537197..51540003-chr3:51571776..51574071,2	MCF-7	breast:
4	chr3:51571369..51573938-chr3:51651321..51654419,3	MCF-7	breast:
5	chr3:51532461..51534963-chr3:51570709..51574166,3	K562	blood:
6	chr3:51563197..51565095-chr3:51570148..51572245,2	K562	blood:
7	chr3:51534724..51536284-chr3:51571592..51573333,2	MCF-7	breast:
8	chr3:51569925..51574030-chr3:51574727..51581311,8	MCF-7	breast:
9	chr3:51571143..51574733-chr3:51574758..51577446,3	K562	blood:
10	chr3:51532744..51536241-chr3:51571123..51575595,5	K562	blood:
11	chr3:51424893..51427102-chr3:51572077..51573890,2	MCF-7	breast:

No data

Variant related genes	Relation type
RAD54L2	TF binding region
ENSG00000145050	Chromatin interaction
ENSG00000164080	Chromatin interaction
ENSG00000145041	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12491048	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12495405	1.00[AFR][1000 genomes]
rs2101056	1.00[AFR][1000 genomes]
rs2356298	1.00[EUR][1000 genomes]
rs56729479	1.00[EUR][1000 genomes]
rs61233013	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51571600-51572200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:51571600-51572200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:51571600-51572600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:51571600-51572600	Flanking Active TSS	Dnd41	blood
5	chr3:51571600-51573600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:51571600-51573800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:51571600-51574200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:51571600-51574200	Active TSS	HSMM	muscle
9	chr3:51571600-51574200	Active TSS	NHLF	lung
10	chr3:51571800-51572200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:51571800-51572200	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr3:51571800-51572200	Flanking Active TSS	Colon Smooth Muscle	Colon
13	chr3:51571800-51572200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr3:51571800-51572200	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr3:51571800-51572200	Enhancers	Spleen	Spleen
16	chr3:51571800-51572400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:51571800-51572400	Flanking Active TSS	Colonic Mucosa	Colon
18	chr3:51571800-51572400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr3:51571800-51572400	Flanking Active TSS	Fetal Brain Female	brain
20	chr3:51571800-51572400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:51571800-51572400	Flanking Active TSS	NHEK	skin
22	chr3:51571800-51572600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:51571800-51572600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:51571800-51572600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr3:51571800-51572800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:51571800-51573400	Active TSS	Brain Germinal Matrix	brain
27	chr3:51571800-51573600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr3:51572000-51572200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr3:51572000-51572200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:51572000-51572200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:51572000-51572200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:51572000-51572200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:51572000-51572200	Flanking Active TSS	Brain Substantia Nigra	brain
34	chr3:51572000-51572200	Flanking Active TSS	Fetal Brain Male	brain
35	chr3:51572000-51572200	Flanking Active TSS	Fetal Heart	heart
36	chr3:51572000-51572200	Flanking Active TSS	Fetal Lung	lung
37	chr3:51572000-51572200	Flanking Active TSS	Fetal Muscle Trunk	muscle
38	chr3:51572000-51572200	Flanking Active TSS	Gastric	stomach
39	chr3:51572000-51572200	Flanking Active TSS	Left Ventricle	heart
40	chr3:51572000-51572200	Flanking Active TSS	Lung	lung
41	chr3:51572000-51572200	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr3:51572000-51572200	Flanking Active TSS	Right Atrium	heart
43	chr3:51572000-51572200	Flanking Active TSS	GM12878-XiMat	blood
44	chr3:51572000-51572200	Flanking Bivalent TSS/Enh	HepG2	liver
45	chr3:51572000-51572200	Flanking Active TSS	HMEC	breast
46	chr3:51572000-51572400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:51572000-51572400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:51572000-51572400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:51572000-51572400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:51572000-51572400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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