Variant report

Variant	rs4601580
Chromosome Location	chr1:154394417-154394418
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154392306..154395112-chr1:154429501..154431445,2	MCF-7	breast:
2	chr1:154390689..154395033-chr1:154398195..154400850,6	MCF-7	breast:
3	chr1:154376615..154383856-chr1:154388009..154396723,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction
ENSG00000228013	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs4553185	0.91[JPT][hapmap]
rs4845371	0.91[JPT][hapmap]
rs4845618	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4845625	0.86[JPT][hapmap]
rs6427658	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs6667434	0.87[JPT][hapmap]
rs6689393	0.86[JPT][hapmap]
rs6694817	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7549250	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7549338	0.87[JPT][hapmap]
rs7553796	0.83[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154389000-154395800	Enhancers	Pancreas	Pancrea
3	chr1:154389000-154402800	Enhancers	Stomach Mucosa	stomach
4	chr1:154389200-154397000	Enhancers	Esophagus	oesophagus
5	chr1:154390400-154394600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:154390600-154397400	Enhancers	Brain Angular Gyrus	brain
7	chr1:154390800-154397400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:154390800-154397400	Enhancers	Brain Cingulate Gyrus	brain
9	chr1:154390800-154398000	Enhancers	Placenta	Placenta
10	chr1:154391000-154397200	Enhancers	Brain Substantia Nigra	brain
11	chr1:154391000-154397400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:154391400-154395000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:154391400-154397400	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr1:154391600-154399600	Weak transcription	Brain Germinal Matrix	brain
15	chr1:154392000-154395000	Enhancers	HMEC	breast
16	chr1:154392400-154396000	Weak transcription	Fetal Kidney	kidney
17	chr1:154392600-154394800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:154392600-154395600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:154392600-154395800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:154392600-154395800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:154392600-154396000	Enhancers	Brain Hippocampus Middle	brain
22	chr1:154392600-154396200	Enhancers	Colon Smooth Muscle	Colon
23	chr1:154392600-154396400	Enhancers	Rectal Smooth Muscle	rectum
24	chr1:154392600-154396600	Weak transcription	Fetal Brain Female	brain
25	chr1:154392600-154397000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:154392600-154397200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:154392800-154394800	Enhancers	NHEK	skin
28	chr1:154392800-154395200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:154392800-154395400	Weak transcription	HSMMtube	muscle
30	chr1:154392800-154395800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:154392800-154395800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:154392800-154396400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:154392800-154396600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:154392800-154396800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:154392800-154397200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr1:154392800-154397200	Enhancers	Adipose Nuclei	Adipose
37	chr1:154392800-154397200	Enhancers	A549	lung
38	chr1:154392800-154397400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:154392800-154397400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:154392800-154397400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:154392800-154397400	Enhancers	NHDF-Ad	bronchial
42	chr1:154392800-154398000	Enhancers	Duodenum Mucosa	Duodenum
43	chr1:154392800-154398800	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr1:154392800-154399600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:154392800-154400200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:154392800-154400600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:154392800-154402800	Weak transcription	Fetal Brain Male	brain
48	chr1:154393000-154395800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:154393000-154396200	Weak transcription	Fetal Lung	lung
50	chr1:154393000-154397000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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