Variant report

Variant	rs28408500
Chromosome Location	chr5:36891001-36891002
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36877699..36879526-chr5:36890759..36893139,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10041439	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10044651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10053695	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10056607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10223124	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11956853	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1389861	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs150537	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs159750	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs159754	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs159911	1.00[AMR][1000 genomes]
rs159912	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294691	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294692	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294693	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs294698	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs297538	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs298970	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs300047	1.00[AMR][1000 genomes]
rs300048	1.00[AMR][1000 genomes]
rs300056	1.00[AMR][1000 genomes]
rs300057	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs300059	1.00[AMR][1000 genomes]
rs301858	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs301900	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs391366	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs463041	1.00[AMR][1000 genomes]
rs55786650	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59774526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6863784	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73750906	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73750908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7702256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7724311	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7735990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9292646	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9764719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv532133	chr5:36834932-36906436	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
5	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv830264	chr5:36887002-36941494	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36879800-36891400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:36880000-36891200	Weak transcription	Fetal Brain Female	brain
3	chr5:36880000-36897400	Weak transcription	NHLF	lung
4	chr5:36880400-36897800	Weak transcription	HUVEC	blood vessel
5	chr5:36881000-36899800	Weak transcription	Brain Substantia Nigra	brain
6	chr5:36881000-36900600	Weak transcription	Osteobl	bone
7	chr5:36881200-36892400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:36881200-36900400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:36881400-36897400	Weak transcription	NHDF-Ad	bronchial
10	chr5:36881800-36895400	Weak transcription	Fetal Kidney	kidney
11	chr5:36882400-36899800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:36882800-36891400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:36884000-36892000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:36884600-36897200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:36885000-36899200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:36886000-36894800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr5:36886200-36891400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:36886200-36891400	Weak transcription	Aorta	Aorta
19	chr5:36886200-36891400	Weak transcription	HSMM	muscle
20	chr5:36886200-36893200	Weak transcription	Placenta	Placenta
21	chr5:36886200-36893400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:36886200-36893400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:36886200-36893600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:36886200-36894800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:36886200-36895000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:36886200-36897600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:36886200-36899000	Weak transcription	Fetal Thymus	thymus
28	chr5:36886400-36893000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:36886400-36893400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:36886400-36893600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:36886400-36893600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:36886400-36894800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:36886400-36896600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:36886400-36897600	Weak transcription	A549	lung
35	chr5:36886400-36898200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr5:36886400-36900400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:36886400-36904800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:36886600-36891400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:36886600-36891400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:36886600-36893000	Weak transcription	Fetal Stomach	stomach
41	chr5:36886600-36894800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:36886600-36895200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:36886600-36896800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:36886600-36896800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr5:36886600-36897200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:36886600-36898600	Weak transcription	Esophagus	oesophagus
47	chr5:36886600-36898600	Weak transcription	Fetal Intestine Small	intestine
48	chr5:36886600-36899800	Weak transcription	Brain Angular Gyrus	brain
49	chr5:36886600-36904800	Weak transcription	Right Ventricle	heart
50	chr5:36886600-36909200	Weak transcription	Left Ventricle	heart

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