Variant report

Variant	rs10015477
Chromosome Location	chr4:87814053-87814054
allele	A/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	MAX	chr4:87812832-87814138	SK-N-SH	brain:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
2	NFIC	chr4:87812795-87814149	ECC-1	luminal epithelium:	n/a	n/a
3	MAX	chr4:87812702-87814495	A549	lung:	n/a	chr4:87814264-87814273 chr4:87813496-87813506 chr4:87813498-87813507
4	MAX	chr4:87812826-87814057	H1-hESC	embryonic stem cell:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
5	MAX	chr4:87812810-87814072	MCF-7	breast:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
6	POLR2A	chr4:87812775-87814378	SK-N-MC	brain:	n/a	n/a
7	REST	chr4:87812960-87814304	H1-neurons	neurons:	n/a	chr4:87813462-87813476
8	MAX	chr4:87812958-87814078	K562	blood:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
9	YY1	chr4:87813561-87814163	SK-N-SH_RA	brain:	n/a	chr4:87813697-87813711 chr4:87813625-87813636
10	E2F6	chr4:87812801-87814131	H1-hESC	embryonic stem cell:	n/a	chr4:87813546-87813557 chr4:87813032-87813039 chr4:87813412-87813422 chr4:87813413-87813423
11	POLR2A	chr4:87811908-87814514	MCF10A-Er-Src	breast:	n/a	n/a
12	MAX	chr4:87812846-87814160	ECC-1	luminal epithelium:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
13	MAX	chr4:87813332-87814104	SK-N-SH	brain:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
14	E2F6	chr4:87812848-87814066	A549	lung:	n/a	chr4:87813546-87813557 chr4:87813032-87813039 chr4:87813412-87813422 chr4:87813413-87813423
15	TCF12	chr4:87812908-87814065	ECC-1	luminal epithelium:	n/a	chr4:87813332-87813339 chr4:87813361-87813369
16	NFIC	chr4:87812843-87814138	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr4:87812746-87814060	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr4:87812927-87814090	HepG2	liver:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
19	E2F6	chr4:87812977-87814089	K562	blood:	n/a	chr4:87813546-87813557 chr4:87813032-87813039 chr4:87813412-87813422 chr4:87813413-87813423
20	POLR2A	chr4:87812701-87814253	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr4:87812852-87814085	H1-hESC	embryonic stem cell:	n/a	chr4:87813412-87813426 chr4:87813493-87813512 chr4:87813492-87813512 chr4:87813025-87813036 chr4:87813505-87813519 chr4:87813697-87813711 chr4:87813409-87813423 chr4:87813625-87813636
22	TCF12	chr4:87812813-87814056	ECC-1	luminal epithelium:	n/a	chr4:87813332-87813339 chr4:87813361-87813369
23	POLR2A	chr4:87811922-87814419	MCF10A-Er-Src	breast:	n/a	n/a
24	MAX	chr4:87812823-87814133	A549	lung:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
25	MAX	chr4:87812954-87814054	A549	lung:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
26	KAP1	chr4:87812763-87814219	HEK293	kidney:	n/a	n/a
27	MYC	chr4:87812497-87814252	A549	lung:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
28	SIN3A	chr4:87812929-87814152	H1-hESC	embryonic stem cell:	n/a	n/a
29	MXI1	chr4:87812622-87814483	SK-N-SH	brain:	n/a	n/a
30	MAX	chr4:87812788-87814115	ECC-1	luminal epithelium:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
31	MAX	chr4:87812848-87814088	HepG2	liver:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
32	MAX	chr4:87812740-87814161	HCT-116	colon:	n/a	chr4:87813496-87813506 chr4:87813498-87813507
33	RCOR1	chr4:87813844-87814115	K562	blood:	n/a	n/a
34	RAD21	chr4:87812908-87814078	IMR90	lung:	n/a	n/a
35	MXI1	chr4:87812467-87814206	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87515391..87517685-chr4:87812251..87815383,4	MCF-7	breast:
2	chr4:87514124..87517809-chr4:87811943..87814768,5	MCF-7	breast:

Variant related genes	Relation type
C4orf36	TF binding region
ENSG00000109339	Chromatin interaction
ENSG00000163629	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10011798	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10015121	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10021020	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10021790	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10034336	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1010902	0.97[ASN][1000 genomes]
rs1010903	0.97[ASN][1000 genomes]
rs13115795	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13120981	0.94[ASN][1000 genomes]
rs13137483	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17012132	0.86[ASN][1000 genomes]
rs1985944	0.97[ASN][1000 genomes]
rs2121871	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28446826	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs28641910	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650493	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716151	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35428486	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs55698195	0.88[ASN][1000 genomes]
rs56201068	0.92[ASN][1000 genomes]
rs6823051	0.97[ASN][1000 genomes]
rs6846822	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72667703	0.97[ASN][1000 genomes]
rs72667705	0.96[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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87812000-87814400	Active TSS	Esophagus	oesophagus
2	chr4:87812600-87814200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr4:87812600-87814200	Active TSS	Brain Angular Gyrus	brain
4	chr4:87812600-87814200	Active TSS	Fetal Intestine Large	intestine
5	chr4:87812600-87814400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:87812600-87814400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr4:87812800-87814200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:87812800-87814200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:87812800-87814200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:87812800-87814200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr4:87812800-87814200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:87812800-87814200	Active TSS	Aorta	Aorta
13	chr4:87812800-87814200	Active TSS	Duodenum Mucosa	Duodenum
14	chr4:87812800-87814200	Active TSS	Right Ventricle	heart
15	chr4:87812800-87814400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr4:87813000-87814200	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr4:87813000-87814200	Active TSS	Fetal Kidney	kidney
18	chr4:87813000-87814400	Flanking Active TSS	HMEC	breast
19	chr4:87813200-87814200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:87813200-87814200	Active TSS	Fetal Intestine Small	intestine
21	chr4:87813200-87814200	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr4:87813400-87814200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
23	chr4:87813400-87814200	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
24	chr4:87813400-87814400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:87813600-87814200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:87813600-87814600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:87813800-87814200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:87813800-87814200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
29	chr4:87813800-87814200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr4:87813800-87814200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
31	chr4:87813800-87814200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:87813800-87814200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
33	chr4:87813800-87814200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr4:87813800-87814200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
35	chr4:87813800-87814200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr4:87813800-87814200	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr4:87813800-87814200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr4:87813800-87814200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr4:87813800-87814200	ZNF genes & repeats	Fetal Brain Male	brain
40	chr4:87813800-87814200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr4:87813800-87814200	Flanking Active TSS	Fetal Thymus	thymus
42	chr4:87813800-87814200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr4:87813800-87814200	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr4:87813800-87814200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr4:87813800-87814200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr4:87813800-87814200	Flanking Active TSS	K562	blood
47	chr4:87813800-87814200	Flanking Active TSS	NHEK	skin
48	chr4:87813800-87814400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:87813800-87814400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:87813800-87814400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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