Variant report

Variant	rs28712413
Chromosome Location	chr4:56292113-56292114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56290594..56293153-chr4:56313887..56316128,2	K562	blood:
2	chr4:56283281..56286016-chr4:56289433..56292166,2	K562	blood:
3	chr4:56252794..56254836-chr4:56291101..56293839,2	MCF-7	breast:
4	chr4:56290006..56292767-chr4:56303276..56306069,2	K562	blood:
5	chr4:56291300..56293587-chr4:56293603..56296458,3	MCF-7	breast:
6	chr4:56290475..56293210-chr4:56296555..56300066,4	K562	blood:

Variant related genes	Relation type
ENSG00000134852	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000273257	Chromatin interaction
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10010919	0.85[AFR][1000 genomes]
rs10016977	1.00[AFR][1000 genomes]
rs10026202	0.80[AFR][1000 genomes]
rs10031345	0.80[AFR][1000 genomes]
rs10155441	0.85[AFR][1000 genomes]
rs11133401	0.81[AFR][1000 genomes]
rs11727642	0.80[AFR][1000 genomes]
rs28369166	0.85[AFR][1000 genomes]
rs28375674	0.81[AFR][1000 genomes]
rs28376882	0.91[AFR][1000 genomes]
rs28391333	0.80[AFR][1000 genomes]
rs28401668	0.90[AFR][1000 genomes]
rs28418730	0.85[AFR][1000 genomes]
rs28456193	0.81[AFR][1000 genomes]
rs28547142	0.81[AFR][1000 genomes]
rs28548946	0.81[AFR][1000 genomes]
rs28588862	0.80[AFR][1000 genomes]
rs28590090	0.81[AFR][1000 genomes]
rs28606621	1.00[AFR][1000 genomes]
rs28683692	0.81[AFR][1000 genomes]
rs34401111	0.81[AFR][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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56264800-56292200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:56269000-56311400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr4:56274600-56332200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:56275600-56292400	Weak transcription	Stomach Mucosa	stomach
7	chr4:56275800-56300000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:56275800-56302200	Strong transcription	Fetal Thymus	thymus
9	chr4:56276000-56302400	Strong transcription	Dnd41	blood
10	chr4:56276000-56320000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:56276200-56292400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:56276200-56296800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:56276200-56304400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:56276200-56310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:56276400-56297800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:56276600-56296400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:56276600-56303400	Strong transcription	Osteobl	bone
18	chr4:56276600-56305000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr4:56277000-56292600	Weak transcription	Fetal Heart	heart
20	chr4:56277000-56296800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:56277400-56302400	Strong transcription	HSMM	muscle
22	chr4:56277400-56306000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:56277600-56301800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:56277600-56305000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:56277800-56293200	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr4:56277800-56302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:56278200-56301000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:56279000-56293000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:56279000-56294800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:56279000-56300200	Strong transcription	HUVEC	blood vessel
31	chr4:56279000-56321800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:56279200-56296200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr4:56280000-56304800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:56280200-56296400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:56280400-56301000	Strong transcription	GM12878-XiMat	blood
36	chr4:56280600-56292600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:56280600-56294800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr4:56280600-56296200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:56280600-56300000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr4:56280600-56301400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr4:56280600-56302000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:56280600-56302200	Strong transcription	Primary B cells from cord blood	blood
43	chr4:56280600-56303400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr4:56280600-56305000	Strong transcription	Placenta	Placenta
45	chr4:56280600-56305200	Strong transcription	Adipose Nuclei	Adipose
46	chr4:56280800-56292600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:56280800-56304800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr4:56280800-56311000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:56281000-56293000	Strong transcription	HepG2	liver
50	chr4:56281000-56293200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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