Variant report

Variant	rs28461705
Chromosome Location	chr7:5254479-5254480
allele	C/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	POLR2A	chr7:5254316-5254699	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5252206..5255144-chr7:5256195..5258471,2	MCF-7	breast:

Variant related genes	Relation type
WIPI2	TF binding region
ENSG00000157954	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10225429	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10225919	1.00[AMR][1000 genomes]
rs10242373	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10243571	1.00[AMR][1000 genomes]
rs10245417	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10249285	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10252983	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10253380	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10270945	1.00[AMR][1000 genomes]
rs10273014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10279924	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28411908	1.00[AMR][1000 genomes]
rs28447119	1.00[AMR][1000 genomes]
rs28450156	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28545115	1.00[AMR][1000 genomes]
rs6979367	1.00[AMR][1000 genomes]
rs73316646	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
3	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
4	nsv1031007	chr7:5101766-5262695	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS 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 target site	19 gene(s)	inside rSNPs	diseases
5	nsv916396	chr7:5128917-5370805	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
7	nsv1015639	chr7:5209510-5255399	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv887390	chr7:5224407-5411296	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases
10	nsv830889	chr7:5248157-5427465	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5231400-5279800	Weak transcription	Fetal Brain Male	brain
2	chr7:5231800-5273400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:5232000-5257200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr7:5232200-5256600	Weak transcription	Small Intestine	intestine
5	chr7:5232400-5256200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:5233000-5255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:5234000-5274800	Weak transcription	Stomach Mucosa	stomach
8	chr7:5237400-5257400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr7:5237400-5258200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:5237400-5272600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr7:5237400-5273400	Strong transcription	Dnd41	blood
12	chr7:5239000-5267800	Strong transcription	Fetal Intestine Large	intestine
13	chr7:5239000-5270800	Strong transcription	Placenta	Placenta
14	chr7:5241000-5265600	Weak transcription	Psoas Muscle	Psoas
15	chr7:5242800-5255200	Weak transcription	Fetal Heart	heart
16	chr7:5242800-5256400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr7:5246400-5271400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:5247800-5270000	Strong transcription	Primary T cells from cord blood	blood
19	chr7:5248000-5257200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr7:5248400-5257000	Strong transcription	GM12878-XiMat	blood
21	chr7:5248400-5273200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:5248800-5257600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr7:5248800-5257800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr7:5248800-5259000	Strong transcription	Fetal Lung	lung
25	chr7:5248800-5267800	Strong transcription	Thymus	Thymus
26	chr7:5248800-5270600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:5248800-5272000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr7:5248800-5272200	Strong transcription	Fetal Muscle Leg	muscle
29	chr7:5248800-5272400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:5249000-5257200	Strong transcription	K562	blood
31	chr7:5249000-5257600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:5249000-5258000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:5249000-5259000	Strong transcription	HepG2	liver
34	chr7:5249000-5259600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr7:5249000-5259800	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr7:5249000-5260000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:5249000-5269200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:5249000-5269200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr7:5249000-5269600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr7:5249000-5269800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr7:5249000-5271200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr7:5249000-5272600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:5249000-5272800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:5249000-5272800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:5249000-5273000	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr7:5249000-5273200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr7:5249000-5273600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:5249000-5273600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr7:5249200-5259000	Strong transcription	Pancreas	Pancrea
50	chr7:5249200-5259200	Strong transcription	Rectal Mucosa Donor 31	rectum

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