Variant report

Variant	rs28573681
Chromosome Location	chr5:43089234-43089235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43088172..43091002-chr5:43120400..43123086,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10051990	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10052644	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10054331	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10056822	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10064210	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10071791	1.00[EUR][1000 genomes]
rs10077219	0.82[AFR][1000 genomes]
rs1122510	1.00[EUR][1000 genomes]
rs13357786	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13360205	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28490330	0.82[AFR][1000 genomes]
rs28628732	0.84[EUR][1000 genomes]
rs56917209	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58980582	0.92[EUR][1000 genomes]
rs60608708	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6451666	0.92[EUR][1000 genomes]
rs6451670	0.96[EUR][1000 genomes]
rs6858989	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6886503	1.00[EUR][1000 genomes]
rs7728625	0.88[EUR][1000 genomes]
rs9292865	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43070000-43105400	Weak transcription	HSMMtube	muscle
2	chr5:43071800-43091000	Weak transcription	Colon Smooth Muscle	Colon
3	chr5:43071800-43091600	Weak transcription	Ovary	ovary
4	chr5:43071800-43096000	Weak transcription	Aorta	Aorta
5	chr5:43071800-43098400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:43071800-43101600	Weak transcription	Esophagus	oesophagus
7	chr5:43071800-43105400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr5:43072400-43104200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:43075600-43096600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:43075600-43101600	Weak transcription	Left Ventricle	heart
11	chr5:43075600-43105000	Weak transcription	NHLF	lung
12	chr5:43075600-43105400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:43075600-43105400	Weak transcription	Psoas Muscle	Psoas
14	chr5:43075800-43096200	Weak transcription	Lung	lung
15	chr5:43075800-43103000	Weak transcription	Spleen	Spleen
16	chr5:43075800-43105400	Weak transcription	Right Ventricle	heart
17	chr5:43075800-43105600	Weak transcription	Pancreas	Pancrea
18	chr5:43076000-43104200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:43076200-43096400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:43076200-43105400	Weak transcription	Brain Angular Gyrus	brain
21	chr5:43076400-43093400	Weak transcription	GM12878-XiMat	blood
22	chr5:43076400-43099800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr5:43076600-43092800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:43076600-43096600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:43077800-43104600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:43078600-43104200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:43079400-43089600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:43079400-43105400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr5:43080200-43105600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr5:43080400-43091000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr5:43080800-43089400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:43080800-43104600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:43081000-43105600	Weak transcription	Brain Germinal Matrix	brain
34	chr5:43081200-43091000	Weak transcription	Placenta	Placenta
35	chr5:43081200-43093200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:43081200-43105400	Weak transcription	Brain Substantia Nigra	brain
37	chr5:43081200-43105400	Weak transcription	NHDF-Ad	bronchial
38	chr5:43081400-43092800	Weak transcription	Adipose Nuclei	Adipose
39	chr5:43081400-43093600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:43081400-43105400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr5:43081400-43105400	Weak transcription	Brain Anterior Caudate	brain
42	chr5:43081400-43105400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:43081600-43096200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:43081800-43105400	Weak transcription	Brain Hippocampus Middle	brain
45	chr5:43081800-43105400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:43082000-43091000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:43082000-43105400	Weak transcription	Liver	Liver
48	chr5:43082200-43104400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:43082400-43090800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:43082400-43091800	Weak transcription	HSMM	muscle

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