Variant report

Variant	rs13150612
Chromosome Location	chr4:124319055-124319056
allele	C/T
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	MXI1	chr4:124317674-124320156	GM12878	blood:	n/a	n/a
2	RAD21	chr4:124318390-124319064	H1-hESC	embryonic stem cell:	n/a	chr4:124318546-124318556
3	MTA3	chr4:124318981-124319460	GM12878	blood:	n/a	n/a
4	EP300	chr4:124318909-124319429	GM12878	blood:	n/a	n/a
5	MAX	chr4:124318419-124319750	HepG2	liver:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
6	CTCF	chr4:124318980-124319130	HCT-116	colon:	n/a	n/a
7	E2F6	chr4:124318349-124319817	H1-hESC	embryonic stem cell:	n/a	chr4:124319515-124319524 chr4:124319515-124319527 chr4:124319715-124319724 chr4:124319509-124319518
8	ZNF384	chr4:124318986-124319096	K562	blood:	n/a	n/a
9	TCF12	chr4:124318258-124320535	ECC-1	luminal epithelium:	n/a	chr4:124319740-124319747 chr4:124318543-124318551 chr4:124318678-124318688
10	EBF1	chr4:124318847-124319055	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:124317591-124321155	HL-60	blood:	n/a	n/a
12	CTBP2	chr4:124318422-124320909	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr4:124318960-124319110	NHEK	skin:	n/a	n/a
14	POLR2A	chr4:124317669-124319432	HepG2	liver:	n/a	n/a
15	BHLHE40	chr4:124318394-124321321	GM12878	blood:	n/a	chr4:124319567-124319583 chr4:124319731-124319747 chr4:124319756-124319772 chr4:124319602-124319618
16	MXI1	chr4:124317273-124321457	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr4:124317699-124320893	HEK293	kidney:	n/a	n/a
18	MAX	chr4:124318297-124319835	K562	blood:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
19	CCNT2	chr4:124318601-124319724	K562	blood:	n/a	chr4:124319515-124319524
20	MYC	chr4:124317439-124319747	MCF10A-Er-Src	breast:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
21	MAX	chr4:124317659-124319856	SK-N-SH	brain:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
22	CHD2	chr4:124317690-124319228	H1-hESC	embryonic stem cell:	n/a	chr4:124318677-124318687
23	MYC	chr4:124317619-124321435	NB4	blood:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
24	YY1	chr4:124319023-124319957	HepG2	liver:	n/a	chr4:124319510-124319521 chr4:124319509-124319518 chr4:124319850-124319864 chr4:124319512-124319521 chr4:124319510-124319524 chr4:124319509-124319523 chr4:124319601-124319610 chr4:124319515-124319524 chr4:124319516-124319527 chr4:124319602-124319616 chr4:124319644-124319658
25	MAX	chr4:124318333-124320311	H1-hESC	embryonic stem cell:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
26	MAX	chr4:124318427-124319732	HUVEC	blood vessel:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
27	BHLHE40	chr4:124317679-124320258	HepG2	liver:	n/a	chr4:124319567-124319583 chr4:124319731-124319747 chr4:124319756-124319772 chr4:124319602-124319618
28	ZNF263	chr4:124317611-124321479	HEK293-T-REx	kidney:	n/a	chr4:124320581-124320590 chr4:124317910-124317931
29	POLR2A	chr4:124317516-124324681	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr4:124318963-124319268	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr4:124318403-124319212	HepG2	liver:	n/a	n/a
32	MAX	chr4:124318239-124319825	MCF-7	breast:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
33	TAF1	chr4:124317737-124319126	ECC-1	luminal epithelium:	n/a	n/a
34	TAF1	chr4:124318881-124319137	SK-N-SH	brain:	n/a	n/a
35	HA-E2F1	chr4:124318427-124320649	MCF-7	breast:	n/a	chr4:124319515-124319524 chr4:124319515-124319527 chr4:124319955-124319964 chr4:124319715-124319724 chr4:124319509-124319518
36	MAX	chr4:124317664-124321158	HepG2	liver:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
37	TEAD4	chr4:124317610-124319211	ECC-1	luminal epithelium:	n/a	n/a
38	MAZ	chr4:124317421-124321556	IMR90	lung:	n/a	chr4:124319645-124319655 chr4:124319507-124319517
39	E2F6	chr4:124318477-124319839	K562	blood:	n/a	chr4:124319515-124319524 chr4:124319515-124319527 chr4:124319715-124319724 chr4:124319509-124319518
40	BACH1	chr4:124318366-124319418	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr4:124318450-124319852	A549	lung:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
42	POLR2A	chr4:124317618-124321804	PANC-1	pancreas:	n/a	n/a
43	SP4	chr4:124318734-124319184	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr4:124318942-124320032	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr4:124317752-124321674	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr4:124317765-124321517	MCF10A-Er-Src	breast:	n/a	n/a
47	SETDB1	chr4:124318459-124319928	K562	blood:	n/a	n/a
48	MAX	chr4:124317667-124319744	SK-N-SH	brain:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
49	MAX	chr4:124317610-124321006	A549	lung:	n/a	chr4:124318656-124318666 chr4:124319645-124319655 chr4:124319507-124319517
50	HEY1	chr4:124317612-124321355	HepG2	liver:	n/a	chr4:124319753-124319768 chr4:124319591-124319600 chr4:124319710-124319725 chr4:124319510-124319525

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:124318366..124320000-chr4:124320399..124322395,2	MCF-7	breast:
2	chr4:124317259..124319394-chr4:124319799..124323152,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPATA5-7	chr4:124318766-124319492	NONHSAT098183

Variant related genes	Relation type
SPRY1	TF binding region
ENSG00000164056	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10518414	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098709	0.91[ASN][1000 genomes]
rs13145927	0.91[ASN][1000 genomes]
rs188513	0.89[ASN][1000 genomes]
rs28477228	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28514996	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300555	0.93[ASN][1000 genomes]
rs300572	0.96[ASN][1000 genomes]
rs300573	0.82[ASN][1000 genomes]
rs300574	0.97[ASN][1000 genomes]
rs4833277	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4833278	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992811	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006945	chr4:124206328-124503863	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv537240	chr4:124206328-124503863	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv3442616	chr4:124318327-124320875	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr4:124317000-124322000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:124317200-124323000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr4:124317400-124319400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:124317400-124319600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:124317400-124320000	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr4:124317400-124320800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:124317400-124320800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:124317400-124321200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:124317400-124321400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:124317400-124321600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr4:124317400-124321800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:124317400-124322000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:124317400-124322200	Active TSS	Adipose Nuclei	Adipose
14	chr4:124317400-124322200	Active TSS	Fetal Kidney	kidney
15	chr4:124317400-124322200	Active TSS	Fetal Lung	lung
16	chr4:124317400-124322400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:124317400-124322400	Active TSS	Brain Anterior Caudate	brain
18	chr4:124317400-124322400	Active TSS	Fetal Intestine Large	intestine
19	chr4:124317400-124322400	Active TSS	Stomach Smooth Muscle	stomach
20	chr4:124317400-124322600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr4:124317400-124322600	Active TSS	Colon Smooth Muscle	Colon
22	chr4:124317400-124322600	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr4:124317400-124322600	Active TSS	Psoas Muscle	Psoas
24	chr4:124317400-124322800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:124317400-124322800	Active TSS	Aorta	Aorta
26	chr4:124317400-124322800	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr4:124317400-124322800	Active TSS	NHLF	lung
28	chr4:124317400-124323200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:124317400-124327000	Active TSS	Right Atrium	heart
30	chr4:124317600-124319200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:124317600-124319200	Active TSS	Right Ventricle	heart
32	chr4:124317600-124319200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr4:124317600-124319400	ZNF genes & repeats	Fetal Brain Male	brain
34	chr4:124317600-124319800	Active TSS	Placenta Amnion	Placenta Amnion
35	chr4:124317600-124320000	Active TSS	Fetal Brain Female	brain
36	chr4:124317600-124320200	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr4:124317600-124320600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr4:124317600-124321000	Active TSS	Hela-S3	cervix
39	chr4:124317600-124321200	Active TSS	Fetal Heart	heart
40	chr4:124317600-124321200	Flanking Bivalent TSS/Enh	Dnd41	blood
41	chr4:124317600-124321400	Active TSS	A549	lung
42	chr4:124317600-124321600	Active TSS	H9 Cell Line	embryonic stem cell
43	chr4:124317600-124321600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr4:124317600-124321600	Active TSS	Brain Angular Gyrus	brain
45	chr4:124317600-124321600	Active TSS	Brain Cingulate Gyrus	brain
46	chr4:124317600-124321600	Active TSS	Colonic Mucosa	Colon
47	chr4:124317600-124321600	Active TSS	HSMM	muscle
48	chr4:124317600-124321800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr4:124317600-124321800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:124317600-124321800	Active TSS	Stomach Mucosa	stomach

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