Variant report

Variant	rs1008709
Chromosome Location	chr5:59106176-59106177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:59105772..59106332-chr5:59944917..59945827,2	MCF-7	breast:
2	chr5:59105757..59106471-chr5:59582762..59583638,3	MCF-7	breast:
3	chr5:59105881..59106438-chr5:59456944..59457607,2	MCF-7	breast:
4	chr5:59105509..59106419-chr5:59678283..59679226,3	MCF-7	breast:
5	chr5:59105406..59106391-chr5:59457337..59458134,2	MCF-7	breast:
6	chr5:59098713..59101064-chr5:59105628..59107812,2	MCF-7	breast:
7	chr5:59105946..59106527-chr5:59881839..59882378,2	K562	blood:
8	chr5:59105855..59106437-chr5:59582746..59583636,2	MCF-7	breast:

No data

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1027747	0.80[CEU][hapmap];0.88[CHB][hapmap];0.92[ASN][1000 genomes]
rs10940649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1120533	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11951422	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11956684	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12523468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13168347	0.92[ASN][1000 genomes]
rs13173398	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs168883	0.88[CHB][hapmap]
rs17310599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17311853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17311925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17371174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17830249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2067024	1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2898247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2938780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2938783	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2938786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963817	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2963818	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2963821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963822	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2963825	0.97[ASN][1000 genomes]
rs2963826	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3111173	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34380238	0.95[ASN][1000 genomes]
rs4700342	0.92[ASN][1000 genomes]
rs56312915	0.98[ASN][1000 genomes]
rs60204066	0.82[ASN][1000 genomes]
rs6885294	0.95[ASN][1000 genomes]
rs72751266	0.98[ASN][1000 genomes]
rs72751270	1.00[ASN][1000 genomes]
rs72751273	0.93[ASN][1000 genomes]
rs72751280	0.98[ASN][1000 genomes]
rs72751283	0.98[ASN][1000 genomes]
rs72751285	0.95[ASN][1000 genomes]
rs72751288	0.96[ASN][1000 genomes]
rs72751293	0.86[ASN][1000 genomes]
rs72751296	0.82[ASN][1000 genomes]
rs72751298	0.82[ASN][1000 genomes]
rs7703963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7718249	0.87[ASN][1000 genomes]
rs7730821	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs986400	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59103400-59107400	Weak transcription	Gastric	stomach
2	chr5:59105800-59106200	Enhancers	Primary B cells from peripheral blood	blood
3	chr5:59105800-59106200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr5:59105800-59106200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr5:59105800-59106400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:59105800-59106400	Active TSS	A549	lung
7	chr5:59106000-59106200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:59106000-59106200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:59106000-59106200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:59106000-59106200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:59106000-59106200	Enhancers	Primary hematopoietic stem cells	blood
12	chr5:59106000-59106200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
13	chr5:59106000-59106200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr5:59106000-59106200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:59106000-59106200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:59106000-59106200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr5:59106000-59106200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr5:59106000-59106200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:59106000-59106200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
20	chr5:59106000-59106200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:59106000-59106200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:59106000-59106200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:59106000-59106200	Enhancers	Liver	Liver
24	chr5:59106000-59106200	Enhancers	Brain Germinal Matrix	brain
25	chr5:59106000-59106200	Enhancers	Duodenum Mucosa	Duodenum
26	chr5:59106000-59106200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr5:59106000-59106200	Flanking Active TSS	Fetal Lung	lung
28	chr5:59106000-59106200	Enhancers	Fetal Muscle Trunk	muscle
29	chr5:59106000-59106200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr5:59106000-59106200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr5:59106000-59106200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr5:59106000-59106200	Flanking Active TSS	Dnd41	blood
33	chr5:59106000-59106200	Flanking Active TSS	HSMMtube	muscle
34	chr5:59106000-59106200	Enhancers	K562	blood
35	chr5:59106000-59106200	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr5:59106000-59106200	Flanking Active TSS	NHDF-Ad	bronchial
37	chr5:59106000-59106200	Flanking Active TSS	Osteobl	bone
38	chr5:59106000-59106400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr5:59106000-59106400	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr5:59106000-59106400	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:59106000-59106400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr5:59106000-59106400	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr5:59106000-59106400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:59106000-59106400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:59106000-59106400	Active TSS	Adipose Nuclei	Adipose
46	chr5:59106000-59106400	Active TSS	Brain Angular Gyrus	brain
47	chr5:59106000-59106400	Active TSS	Brain Anterior Caudate	brain
48	chr5:59106000-59106400	Active TSS	Brain Hippocampus Middle	brain
49	chr5:59106000-59106400	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr5:59106000-59106400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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