Variant report

Variant	rs56190569
Chromosome Location	chr3:155463068-155463069
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:155462802-155463089	MCF-7	breast:	n/a	chr3:155462885-155462895
2	SP1	chr3:155462360-155463230	HCT-116	colon:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
3	CTBP2	chr3:155461816-155463206	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr3:155462750-155463087	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD2	chr3:155462631-155463156	H1-hESC	embryonic stem cell:	n/a	n/a
6	SP1	chr3:155462739-155463113	K562	blood:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
7	SP1	chr3:155461843-155463352	A549	lung:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
8	SP1	chr3:155462606-155463205	H1-hESC	embryonic stem cell:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
9	SP1	chr3:155462574-155463173	H1-hESC	embryonic stem cell:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
10	ELF1	chr3:155462106-155463176	MCF-7	breast:	n/a	chr3:155462832-155462841
11	TCF12	chr3:155462610-155463220	ECC-1	luminal epithelium:	n/a	n/a
12	CREB1	chr3:155462768-155463177	A549	lung:	n/a	n/a
13	YY1	chr3:155462728-155463124	H1-hESC	embryonic stem cell:	n/a	chr3:155462829-155462838 chr3:155462832-155462841
14	POLR2A	chr3:155461711-155463117	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr3:155461782-155463169	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3A	chr3:155461524-155463101	H1-hESC	embryonic stem cell:	n/a	n/a
17	BACH1	chr3:155462057-155463080	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:155461880-155463078	MCF-7	breast:	n/a	n/a
19	POU5F1	chr3:155462673-155463150	H1-hESC	embryonic stem cell:	n/a	chr3:155462850-155462864 chr3:155462851-155462865 chr3:155462850-155462864 chr3:155462850-155462864
20	E2F6	chr3:155462750-155463169	A549	lung:	n/a	chr3:155462857-155462866
21	CREB1	chr3:155462159-155463115	HepG2	liver:	n/a	n/a
22	ELF1	chr3:155462762-155463124	A549	lung:	n/a	chr3:155462832-155462841
23	HA-E2F1	chr3:155461710-155463204	MCF-7	breast:	n/a	chr3:155462003-155462012 chr3:155462857-155462866
24	CEBPD	chr3:155462655-155463101	HepG2	liver:	n/a	n/a
25	YY1	chr3:155462704-155463146	K562	blood:	n/a	chr3:155462829-155462838 chr3:155462832-155462841
26	CREB1	chr3:155462676-155463086	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr3:155462920-155463070	HAc	cerebellar:	n/a	n/a
28	MYC	chr3:155462871-155463184	MCF10A-Er-Src	breast:	n/a	chr3:155462885-155462895
29	POLR2A	chr3:155462427-155463087	ProgFib	skin:	n/a	n/a
30	EBF1	chr3:155462961-155463332	GM12878	blood:	n/a	n/a
31	TEAD4	chr3:155462774-155463101	H1-hESC	embryonic stem cell:	n/a	n/a
32	ZBTB33	chr3:155462679-155463130	HCT-116	colon:	n/a	n/a
33	RCOR1	chr3:155462698-155463111	K562	blood:	n/a	n/a
34	TCF7L2	chr3:155462654-155463097	HCT-116	colon:	n/a	n/a
35	TBP	chr3:155462711-155463099	HepG2	liver:	n/a	n/a
36	MYC	chr3:155462671-155463112	K562	blood:	n/a	chr3:155462885-155462895
37	MYBL2	chr3:155462587-155463183	HepG2	liver:	n/a	n/a
38	CEBPB	chr3:155462962-155463280	K562	blood:	n/a	n/a
39	REST	chr3:155461339-155463168	H1-neurons	neurons:	n/a	chr3:155462231-155462244 chr3:155462011-155462024
40	MAZ	chr3:155462279-155463294	IMR90	lung:	n/a	chr3:155462885-155462895
41	MAX	chr3:155462671-155463123	SK-N-SH	brain:	n/a	chr3:155462885-155462895
42	MAX	chr3:155461818-155463098	ECC-1	luminal epithelium:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
43	YY1	chr3:155462779-155463108	ECC-1	luminal epithelium:	n/a	chr3:155462829-155462838 chr3:155462832-155462841
44	MAX	chr3:155462756-155463104	K562	blood:	n/a	chr3:155462885-155462895
45	MAZ	chr3:155462636-155463101	HepG2	liver:	n/a	chr3:155462885-155462895
46	MYC	chr3:155461949-155463142	K562	blood:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
47	SIN3AK20	chr3:155462676-155463075	SK-N-SH	brain:	n/a	n/a
48	MAX	chr3:155461801-155463231	MCF-7	breast:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
49	JUND	chr3:155462625-155463110	K562	blood:	n/a	n/a
50	POLR2A	chr3:155462609-155463144	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:155461486..155463918-chr3:155586998..155589713,4	K562	blood:
2	chr3:155462983..155464516-chr3:156391624..156393774,2	MCF-7	breast:
3	chr3:155461195..155464539-chr3:155588373..155590107,3	MCF-7	breast:
4	chr3:155460891..155464537-chr3:155570941..155574143,3	MCF-7	breast:
5	chr3:155462054..155464221-chr3:155571081..155573574,2	MCF-7	breast:
6	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:
7	chr3:155461523..155464397-chr3:155587900..155591398,5	MCF-7	breast:

Variant related genes	Relation type
PLCH1	TF binding region
ENSG00000214919	TF binding region
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163655	Chromatin interaction
ENSG00000169359	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13324811	0.89[ASN][1000 genomes]
rs28705686	0.96[EUR][1000 genomes]
rs4680214	0.96[EUR][1000 genomes]
rs62284705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156589	0.94[EUR][1000 genomes]
rs7372113	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618361	0.93[ASN][1000 genomes]
rs7620836	0.93[ASN][1000 genomes]
rs9850228	0.94[EUR][1000 genomes]
rs9853408	0.93[ASN][1000 genomes]
rs9879847	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155460800-155463600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:155461000-155464400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:155461200-155464200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:155461400-155463200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
5	chr3:155461400-155463200	Active TSS	Left Ventricle	heart
6	chr3:155461400-155463200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
7	chr3:155461400-155463200	Bivalent/Poised TSS	HSMM	muscle
8	chr3:155461400-155463400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:155461400-155463400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr3:155461400-155463600	Active TSS	Pancreas	Pancrea
11	chr3:155461400-155463800	Active TSS	Gastric	stomach
12	chr3:155461400-155463800	Active TSS	Right Ventricle	heart
13	chr3:155461400-155463800	Active TSS	A549	lung
14	chr3:155461400-155463800	Active TSS	NHLF	lung
15	chr3:155461400-155464000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr3:155461400-155464000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr3:155461400-155464000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:155461400-155464000	Active TSS	Right Atrium	heart
19	chr3:155461400-155464200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:155461400-155464200	Active TSS	Brain Angular Gyrus	brain
21	chr3:155461400-155464200	Active TSS	Brain Cingulate Gyrus	brain
22	chr3:155461600-155463200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
23	chr3:155461600-155463200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr3:155461600-155463200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
25	chr3:155461600-155463200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:155461600-155463200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr3:155461600-155463200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
28	chr3:155461600-155463400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:155461600-155463400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
30	chr3:155461600-155463400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
31	chr3:155461600-155463600	Active TSS	Brain Substantia Nigra	brain
32	chr3:155461600-155463600	Active TSS	Colon Smooth Muscle	Colon
33	chr3:155461600-155463600	Bivalent/Poised TSS	Thymus	Thymus
34	chr3:155461600-155463800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:155461600-155463800	Active TSS	Aorta	Aorta
36	chr3:155461600-155463800	Active TSS	Ovary	ovary
37	chr3:155461600-155464000	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr3:155461600-155464000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr3:155461600-155464000	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr3:155461600-155464000	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr3:155461600-155464200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:155461600-155464400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr3:155461800-155463200	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr3:155461800-155463200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:155461800-155463200	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr3:155461800-155463200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:155461800-155463200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr3:155461800-155463200	Flanking Bivalent TSS/Enh	Placenta	Placenta
49	chr3:155461800-155463200	Active TSS	K562	blood
50	chr3:155461800-155463400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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