Variant report

Variant	rs878956
Chromosome Location	chr4:56814115-56814116
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	TBL1XR1	chr4:56813237-56814428	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:56813222-56814346	NB4	blood:	n/a	n/a
3	POLR2A	chr4:56814107-56814115	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:56813166-56814454	GM12892	blood:	n/a	n/a
5	POLR2A	chr4:56813528-56814357	GM12891	blood:	n/a	n/a
6	POLR2A	chr4:56813158-56816168	HUVEC	blood vessel:	n/a	n/a
7	TEAD4	chr4:56814077-56815860	K562	blood:	n/a	n/a
8	POLR2A	chr4:56813464-56814334	GM12891	blood:	n/a	n/a
9	POLR2A	chr4:56813218-56814406	GM12891	blood:	n/a	n/a
10	RCOR1	chr4:56813365-56815980	GM12878	blood:	n/a	n/a
11	RELA	chr4:56813238-56816761	GM12891	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
12	STAT1	chr4:56813449-56815671	GM12878	blood:	n/a	chr4:56814229-56814252 chr4:56815369-56815381 chr4:56814365-56814372 chr4:56814975-56814995
13	NRF1	chr4:56813961-56814687	SK-N-SH	brain:	n/a	chr4:56814288-56814299 chr4:56814285-56814299 chr4:56814287-56814298
14	POLR2A	chr4:56813543-56814233	GM12891	blood:	n/a	n/a
15	MTA3	chr4:56813232-56816058	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:56813128-56814507	GM12878	blood:	n/a	n/a
17	NRF1	chr4:56814040-56814532	GM12878	blood:	n/a	chr4:56814288-56814299 chr4:56814285-56814299 chr4:56814287-56814298
18	PML	chr4:56813219-56815891	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:56813356-56816455	GM12892	blood:	n/a	n/a
20	TCF7L2	chr4:56813783-56814394	Hela-S3	cervix:	n/a	n/a
21	ELF1	chr4:56813534-56814235	GM12878	blood:	n/a	n/a
22	RELA	chr4:56814018-56815643	GM18526	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
23	POLR2A	chr4:56813984-56816308	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr4:56814056-56815539	MCF10A-Er-Src	breast:	n/a	chr4:56814229-56814252 chr4:56815369-56815381 chr4:56814365-56814372 chr4:56814975-56814995
25	RELA	chr4:56813567-56816431	GM12892	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
26	POLR2A	chr4:56813317-56816266	IMR90	lung:	n/a	n/a
27	MAFK	chr4:56813927-56814429	K562	blood:	n/a	n/a
28	TBP	chr4:56814023-56814994	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr4:56813683-56815562	SK-N-SH	brain:	n/a	chr4:56814939-56814949 chr4:56814934-56814952 chr4:56813921-56813934 chr4:56814937-56814950 chr4:56814937-56814946 chr4:56813918-56813936 chr4:56814936-56814957 chr4:56814935-56814951 chr4:56813920-56813941
30	POLR2A	chr4:56813906-56815772	U87	brain:	n/a	n/a
31	CHD1	chr4:56813363-56816295	GM12878	blood:	n/a	chr4:56815368-56815378 chr4:56814858-56814868
32	POLR2A	chr4:56813528-56814328	GM12892	blood:	n/a	n/a
33	PML	chr4:56813474-56814251	GM12878	blood:	n/a	n/a
34	RELA	chr4:56813350-56814478	GM18951	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
35	MEF2A	chr4:56813400-56814257	GM12878	blood:	n/a	n/a
36	BCLAF1	chr4:56813494-56814284	GM12878	blood:	n/a	n/a
37	GATA2	chr4:56813691-56814520	HUVEC	blood vessel:	n/a	chr4:56814417-56814427
38	FOS	chr4:56814110-56814541	MCF10A-Er-Src	breast:	n/a	chr4:56814276-56814288
39	POLR2A	chr4:56813123-56816170	HUVEC	blood vessel:	n/a	n/a
40	MAFK	chr4:56813974-56815061	IMR90	lung:	n/a	n/a
41	SPI1	chr4:56813988-56814362	GM12891	blood:	n/a	n/a
42	HCFC1	chr4:56814086-56816232	Hela-S3	cervix:	n/a	n/a
43	TBP	chr4:56813352-56815746	GM12878	blood:	n/a	n/a
44	CHD2	chr4:56813364-56815764	GM12878	blood:	n/a	chr4:56815368-56815378 chr4:56814858-56814868
45	RELA	chr4:56813325-56816613	GM10847	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
46	ATF2	chr4:56813229-56814436	GM12878	blood:	n/a	n/a
47	RELA	chr4:56813401-56814556	GM12878	blood:	n/a	chr4:56814238-56814247 chr4:56814238-56814247
48	EBF1	chr4:56813338-56815387	GM12878	blood:	n/a	chr4:56814935-56814946
49	FOS	chr4:56814048-56814599	MCF10A-Er-Src	breast:	n/a	chr4:56814276-56814288
50	SPI1	chr4:56813967-56814331	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56411182..56412770-chr4:56812130..56814893,2	K562	blood:
2	chr4:56754886..56756394-chr4:56813463..56814975,2	MCF-7	breast:
3	chr4:56813951..56816639-chr4:57299941..57302593,2	K562	blood:
4	chr4:56246727..56248649-chr4:56813928..56816601,2	K562	blood:
5	chr4:56813904..56818311-chr4:57252529..57254894,5	K562	blood:
6	chr4:56812961..56814619-chr4:57166848..57168708,2	K562	blood:
7	chr4:56807427..56809711-chr4:56812377..56814575,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMU-3	chr4:56814006-56814177	NONHSAT096484

Variant related genes	Relation type
CEP135	TF binding region
ENSG00000128059	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000134852	Chromatin interaction
ENSG00000090989	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1823165	0.97[ASN][1000 genomes]
rs1838928	0.82[ASN][1000 genomes]
rs2593075	0.82[ASN][1000 genomes]
rs2702324	0.85[ASN][1000 genomes]
rs6857163	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv964348	chr4:56782802-56815653	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56805200-56814600	Weak transcription	Spleen	Spleen
2	chr4:56810400-56814600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:56812000-56814800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:56812200-56814600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:56812200-56814800	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr4:56812200-56816200	Active TSS	Lung	lung
7	chr4:56812400-56815000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:56812600-56814400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr4:56812600-56816000	Active TSS	Left Ventricle	heart
10	chr4:56812600-56816200	Active TSS	Right Ventricle	heart
11	chr4:56812800-56814400	Active TSS	Stomach Smooth Muscle	stomach
12	chr4:56813000-56814400	Active TSS	HUVEC	blood vessel
13	chr4:56813000-56816800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:56813200-56814200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:56813200-56814200	Active TSS	Fetal Kidney	kidney
16	chr4:56813200-56814400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:56813200-56814400	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr4:56813200-56814600	Active TSS	Fetal Muscle Leg	muscle
19	chr4:56813200-56814800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:56813200-56814800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr4:56813200-56814800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:56813200-56814800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr4:56813200-56814800	Flanking Active TSS	NH-A	brain
24	chr4:56813200-56814800	Flanking Active TSS	Osteobl	bone
25	chr4:56813200-56815000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr4:56813200-56815000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr4:56813200-56815600	Active TSS	Rectal Smooth Muscle	rectum
28	chr4:56813200-56816000	Active TSS	Psoas Muscle	Psoas
29	chr4:56813200-56816000	Active TSS	Right Atrium	heart
30	chr4:56813400-56814200	Enhancers	Brain Cingulate Gyrus	brain
31	chr4:56813400-56814200	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr4:56813400-56814200	Enhancers	Dnd41	blood
33	chr4:56813400-56814200	Flanking Active TSS	NHLF	lung
34	chr4:56813400-56814400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr4:56813400-56814400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr4:56813400-56814400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:56813400-56814400	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr4:56813400-56814600	Enhancers	H9 Cell Line	embryonic stem cell
39	chr4:56813400-56814600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:56813400-56814600	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr4:56813400-56814800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:56813400-56814800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr4:56813400-56814800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr4:56813400-56814800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr4:56813400-56815000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:56813400-56815600	Active TSS	Primary T cells from cord blood	blood
47	chr4:56813400-56816000	Active TSS	Fetal Intestine Small	intestine
48	chr4:56813400-56816200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr4:56813400-56816200	Active TSS	Fetal Muscle Trunk	muscle
50	chr4:56813400-56816800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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