Variant report

Variant	rs6852858
Chromosome Location	chr4:299259-299260
allele	A/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	YY1	chr4:298767-299281	H1-hESC	embryonic stem cell:	n/a	chr4:298993-299004 chr4:299031-299041 chr4:299030-299042 chr4:299027-299036 chr4:298875-298886
2	MYC	chr4:299060-299477	H1-hESC	embryonic stem cell:	n/a	chr4:299290-299300
3	POLR2A	chr4:298946-299517	MCF-7	breast:	n/a	n/a
4	POLR2A	chr4:299121-299319	MCF10A-Er-Src	breast:	n/a	n/a
5	TAF1	chr4:298185-299598	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr4:299033-299610	H1-hESC	embryonic stem cell:	n/a	chr4:299290-299300
7	SP1	chr4:299060-299523	H1-hESC	embryonic stem cell:	n/a	chr4:299332-299353 chr4:299078-299092 chr4:299290-299301
8	MAX	chr4:298635-299666	H1-hESC	embryonic stem cell:	n/a	chr4:299290-299300
9	SIN3A	chr4:298688-299538	H1-hESC	embryonic stem cell:	n/a	chr4:299302-299313
10	E2F6	chr4:298779-299611	H1-hESC	embryonic stem cell:	n/a	chr4:299037-299046 chr4:299038-299045 chr4:299038-299045 chr4:299025-299035 chr4:299038-299045 chr4:298990-299000
11	NANOG	chr4:299178-299543	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr4:298720-299367	MCF-7	breast:	n/a	n/a
13	POLR2A	chr4:299107-299264	GM12878	blood:	n/a	n/a
14	PBX3	chr4:299018-299611	SK-N-SH	brain:	n/a	chr4:299381-299390
15	MAX	chr4:299137-299491	SK-N-SH	brain:	n/a	chr4:299290-299300
16	CEBPB	chr4:299246-299582	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr4:298779-299491	H1-hESC	embryonic stem cell:	n/a	n/a
18	GABPA	chr4:298917-299587	MCF-7	breast:	n/a	n/a
19	E2F6	chr4:298611-299704	H1-hESC	embryonic stem cell:	n/a	chr4:299037-299046 chr4:299038-299045 chr4:299038-299045 chr4:299025-299035 chr4:299038-299045 chr4:298990-299000
20	MXI1	chr4:298677-299543	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr4:298911-299350	MCF-7	breast:	n/a	n/a
22	POLR2A	chr4:297841-299345	H1-hESC	embryonic stem cell:	n/a	n/a
23	CHD2	chr4:298935-299562	H1-hESC	embryonic stem cell:	n/a	n/a
24	SP2	chr4:299071-299618	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:299040-299294	ProgFib	skin:	n/a	n/a
26	MAX	chr4:298639-299604	MCF-7	breast:	n/a	chr4:299290-299300
27	PBX3	chr4:299131-299610	SK-N-SH	brain:	n/a	chr4:299381-299390
28	GABPA	chr4:299105-299518	MCF-7	breast:	n/a	n/a
29	POLR2A	chr4:298663-299577	H1-hESC	embryonic stem cell:	n/a	n/a
30	E2F4	chr4:298661-299614	MCF10A-Er-Src	breast:	n/a	chr4:299037-299046 chr4:299038-299045 chr4:299038-299045 chr4:299025-299035 chr4:299038-299045 chr4:298990-299000
31	MAX	chr4:298877-299652	H1-hESC	embryonic stem cell:	n/a	chr4:299290-299300
32	GTF2F1	chr4:299135-299522	H1-hESC	embryonic stem cell:	n/a	n/a
33	SP4	chr4:299064-299579	H1-hESC	embryonic stem cell:	n/a	chr4:299284-299300 chr4:299290-299301
34	POLR2A	chr4:298696-299375	H1-hESC	embryonic stem cell:	n/a	n/a
35	NFYB	chr4:299220-299489	K562	blood:	n/a	chr4:299339-299354 chr4:299339-299354 chr4:299342-299352 chr4:299340-299354 chr4:299313-299326
36	BACH1	chr4:299051-299498	H1-hESC	embryonic stem cell:	n/a	n/a
37	SP1	chr4:299020-299569	H1-hESC	embryonic stem cell:	n/a	chr4:299332-299353 chr4:299078-299092 chr4:299290-299301
38	POLR2A	chr4:299033-299406	PFSK-1	brain:	n/a	n/a
39	TAF1	chr4:298708-299529	H1-hESC	embryonic stem cell:	n/a	n/a
40	YY1	chr4:298621-299554	H1-hESC	embryonic stem cell:	n/a	chr4:298993-299004 chr4:299031-299041 chr4:299030-299042 chr4:299027-299036 chr4:298875-298886
41	MYC	chr4:299252-299589	MCF10A-Er-Src	breast:	n/a	chr4:299290-299300
42	MXI1	chr4:297847-299637	SK-N-SH	brain:	n/a	n/a
43	SIN3AK20	chr4:299095-299309	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr4:297877-299675	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr4:299063-299263	MCF10A-Er-Src	breast:	n/a	n/a
46	JUND	chr4:299030-299503	H1-hESC	embryonic stem cell:	n/a	chr4:299341-299350
47	POLR2A	chr4:298696-299525	H1-hESC	embryonic stem cell:	n/a	n/a
48	TAF7	chr4:298960-299429	H1-hESC	embryonic stem cell:	n/a	n/a
49	SP2	chr4:299066-299603	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:297745..300703-chr4:329604..332277,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF732-3	chr4:299097-299263	NONHSAT094528

Variant related genes	Relation type
ZNF732	TF binding region
ENSG00000131127	Chromatin interaction
ENSG00000251535	Chromatin interaction

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

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

rs_ID	r²[population]
rs35476693	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518181	0.83[ASN][1000 genomes]
rs73791826	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73791827	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1001899	chr4:68809-517736	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv1010829	chr4:147570-547070	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv536970	chr4:147570-547070	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:297400-299400	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr4:297400-299600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr4:297400-300000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:297400-301600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr4:297600-299400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:297600-299400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:297600-299600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:297600-299600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:297600-299600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
10	chr4:297600-299600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr4:297600-300600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
12	chr4:297600-301000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:297600-301400	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr4:297800-299400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:297800-299400	ZNF genes & repeats	Spleen	Spleen
16	chr4:297800-299600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:298000-299400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:298000-299600	Active TSS	H1 Cell Line	embryonic stem cell
19	chr4:298000-299600	Active TSS	H9 Cell Line	embryonic stem cell
20	chr4:298000-299600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:298000-299600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:298000-299600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr4:298000-299600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:298000-299600	Active TSS	Osteobl	bone
25	chr4:298000-299800	Active TSS	Placenta Amnion	Placenta Amnion
26	chr4:298200-299400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:298200-299400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:298200-299400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:298200-299400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:298200-299400	Active TSS	Fetal Heart	heart
31	chr4:298200-299600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:298200-299600	Active TSS	HMEC	breast
33	chr4:298200-299600	Active TSS	HUVEC	blood vessel
34	chr4:298200-299600	Active TSS	NHEK	skin
35	chr4:298400-299400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
36	chr4:298400-299600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:298400-299600	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr4:298400-299600	Active TSS	Brain Anterior Caudate	brain
39	chr4:298400-299600	Active TSS	Fetal Intestine Small	intestine
40	chr4:298400-299600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
41	chr4:298400-299600	Active TSS	NH-A	brain
42	chr4:298600-299400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:298600-299400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:298600-299400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
45	chr4:298600-299400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:298600-299400	Active TSS	Fetal Kidney	kidney
47	chr4:298600-299400	Flanking Active TSS	Placenta	Placenta
48	chr4:298600-299400	ZNF genes & repeats	Lung	lung
49	chr4:298600-299400	Bivalent/Poised TSS	Psoas Muscle	Psoas
50	chr4:298600-299600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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