Variant report

Variant	rs2904883
Chromosome Location	chr4:120987349-120987350
allele	G/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	NFIC	chr4:120987343-120988574	GM12878	blood:	n/a	n/a
2	MAX	chr4:120987154-120988535	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:120986908-120989985	GM12891	blood:	n/a	n/a
4	POLR2A	chr4:120987337-120989347	GM19099	blood:	n/a	n/a
5	POLR2A	chr4:120987175-120989426	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:120987221-120988829	K562	blood:	n/a	n/a
7	MAX	chr4:120987276-120988610	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr4:120987270-120989178	PFSK-1	brain:	n/a	n/a
9	ZNF384	chr4:120987210-120987935	K562	blood:	n/a	n/a
10	POLR2A	chr4:120987152-120989112	PBDE	blood:	n/a	n/a
11	HEY1	chr4:120987158-120988776	K562	blood:	n/a	n/a
12	POLR2A	chr4:120987075-120989540	K562	blood:	n/a	n/a
13	POLR2A	chr4:120987274-120988852	PFSK-1	brain:	n/a	n/a
14	GTF2F1	chr4:120987340-120989274	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr4:120987226-120988906	HUVEC	blood vessel:	n/a	n/a
16	MYC	chr4:120987347-120988619	Hela-S3	cervix:	n/a	n/a
17	E2F4	chr4:120985855-120988544	MCF10A-Er-Src	breast:	n/a	chr4:120987957-120987968 chr4:120988011-120988020
18	MYC	chr4:120987219-120989379	K562	blood:	n/a	n/a
19	MAX	chr4:120987224-120988870	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr4:120987349-120989466	GM18951	blood:	n/a	n/a
21	MXI1	chr4:120987157-120988818	HepG2	liver:	n/a	n/a
22	RCOR1	chr4:120987314-120987443	Hela-S3	cervix:	n/a	n/a
23	IRF1	chr4:120987340-120988870	K562	blood:	n/a	chr4:120987502-120987516
24	CHD1	chr4:120987329-120987760	H1-hESC	embryonic stem cell:	n/a	n/a
25	CEBPB	chr4:120987082-120988973	Hela-S3	cervix:	n/a	chr4:120988777-120988786 chr4:120988777-120988786 chr4:120988775-120988788 chr4:120988775-120988788 chr4:120988775-120988786 chr4:120988777-120988786 chr4:120988777-120988786 chr4:120987221-120987232 chr4:120988775-120988788 chr4:120987221-120987232 chr4:120988777-120988788
26	MYC	chr4:120986892-120989484	K562	blood:	n/a	n/a
27	MXI1	chr4:120986904-120989097	IMR90	lung:	n/a	n/a
28	MTA3	chr4:120987333-120988954	GM12878	blood:	n/a	n/a
29	CREB1	chr4:120987333-120988926	HepG2	liver:	n/a	n/a
30	RELA	chr4:120987331-120988641	GM19099	blood:	n/a	n/a
31	POLR2A	chr4:120987298-120989288	U87	brain:	n/a	n/a
32	POLR2A	chr4:120987163-120989871	K562	blood:	n/a	n/a
33	POLR2A	chr4:120987299-120988720	HEK293	kidney:	n/a	n/a
34	MXI1	chr4:120986183-120989454	SK-N-SH	brain:	n/a	n/a
35	SIN3A	chr4:120987080-120988768	H1-hESC	embryonic stem cell:	n/a	n/a
36	RELA	chr4:120987261-120989116	GM10847	blood:	n/a	n/a
37	POLR2A	chr4:120987338-120988797	GM12891	blood:	n/a	n/a
38	TCF12	chr4:120987312-120988467	ECC-1	luminal epithelium:	n/a	chr4:120988325-120988332 chr4:120987396-120987403
39	MYBL2	chr4:120987281-120988756	HepG2	liver:	n/a	n/a
40	POLR2A	chr4:120987160-120988844	HL-60	blood:	n/a	n/a
41	MYC	chr4:120987316-120988855	K562	blood:	n/a	n/a
42	MXI1	chr4:120987076-120988642	Hela-S3	cervix:	n/a	n/a
43	MAZ	chr4:120987233-120988959	K562	blood:	n/a	n/a
44	MAX	chr4:120987042-120988801	NB4	blood:	n/a	n/a
45	MAX	chr4:120987140-120988778	K562	blood:	n/a	n/a
46	POLR2A	chr4:120987349-120989227	GM19193	blood:	n/a	n/a
47	E2F6	chr4:120987140-120988669	H1-hESC	embryonic stem cell:	n/a	chr4:120988011-120988020
48	MAX	chr4:120987335-120988890	HepG2	liver:	n/a	n/a
49	POLR2A	chr4:120987326-120989395	K562	blood:	n/a	n/a
50	POLR2A	chr4:120987082-120988819	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:120981267..120985179-chr4:120986108..120989816,4	MCF-7	breast:
2	chr4:120426318..120428351-chr4:120986302..120988038,2	K562	blood:
3	chr4:120131923..120135922-chr4:120985229..120990455,5	K562	blood:
4	chr11:65627173..65627816-chr4:120987298..120987988,2	Hela-S3	cervix:
5	chr4:120548759..120550296-chr4:120986622..120988750,2	K562	blood:
6	chr4:120230931..120233394-chr4:120986011..120987625,2	K562	blood:
7	chr4:120987081..120989411-chr4:129732197..129734433,2	K562	blood:
8	chr4:120131661..120133788-chr4:120986266..120989312,3	K562	blood:
9	chr4:120220396..120223311-chr4:120987092..120990068,3	K562	blood:
10	chr4:120153288..120155840-chr4:120986022..120987789,2	K562	blood:
11	chr15:77712383..77713035-chr4:120987269..120987962,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000250938	TF binding region
ENSG00000164096	Chromatin interaction
ENSG00000178636	Chromatin interaction
ENSG00000140382	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000173517	Chromatin interaction
ENSG00000138735	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000145390	Chromatin interaction
ENSG00000164109	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10010446	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11942060	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12711084	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1972014	0.88[ASN][1000 genomes]
rs28538838	0.88[ASN][1000 genomes]
rs2904884	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2908990	0.87[ASN][1000 genomes]
rs2934379	0.88[ASN][1000 genomes]
rs4834834	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903147	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1007641	chr4:120884220-121555889	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537234	chr4:120884220-121555889	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 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	chr4:120971000-120987400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:120971200-120987400	Weak transcription	Left Ventricle	heart
3	chr4:120985800-120988600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:120985800-120988800	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr4:120986000-120987400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr4:120986000-120988800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:120986000-120988800	Active TSS	HMEC	breast
8	chr4:120986000-120989000	Active TSS	A549	lung
9	chr4:120986000-120989200	Active TSS	K562	blood
10	chr4:120986200-120987600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:120986200-120987600	Flanking Active TSS	HUVEC	blood vessel
12	chr4:120986400-120987400	Active TSS	HepG2	liver
13	chr4:120986400-120988800	Active TSS	Hela-S3	cervix
14	chr4:120986400-120989000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:120986400-120989000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:120986400-120989000	Active TSS	NHDF-Ad	bronchial
17	chr4:120986400-120989200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:120986400-120989200	Active TSS	GM12878-XiMat	blood
19	chr4:120986400-120989400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr4:120986600-120987600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:120986600-120987600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr4:120986600-120987800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:120986600-120988000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:120986600-120988800	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:120986600-120988800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:120986600-120989000	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr4:120986600-120989000	Active TSS	Thymus	Thymus
28	chr4:120986600-120989000	Active TSS	NHLF	lung
29	chr4:120986800-120987400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:120986800-120987400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr4:120986800-120987400	Enhancers	Primary B cells from peripheral blood	blood
32	chr4:120986800-120987400	Flanking Active TSS	Fetal Heart	heart
33	chr4:120986800-120987600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr4:120986800-120987600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr4:120986800-120987800	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr4:120986800-120987800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:120986800-120987800	Flanking Active TSS	NH-A	brain
38	chr4:120986800-120988000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr4:120986800-120988800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:120986800-120988800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:120986800-120988800	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr4:120986800-120988800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:120986800-120988800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:120986800-120989000	Active TSS	H9 Cell Line	embryonic stem cell
45	chr4:120986800-120989400	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr4:120986800-120989800	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr4:120987000-120987400	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr4:120987000-120987400	Flanking Active TSS	Fetal Lung	lung
49	chr4:120987000-120987600	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr4:120987000-120987600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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