Variant report

Variant	rs17452287
Chromosome Location	chr1:56107056-56107057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1039294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10493193	0.85[CEU][hapmap]
rs10493194	0.85[CEU][hapmap]
rs10493195	0.85[CEU][hapmap]
rs11206626	0.85[CEU][hapmap]
rs11206635	0.92[CEU][hapmap]
rs11206649	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11801001	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11805740	0.92[CEU][hapmap]
rs12116670	0.85[CEU][hapmap]
rs12117758	0.85[CEU][hapmap]
rs12124658	0.90[EUR][1000 genomes]
rs12125730	0.90[CEU][hapmap]
rs12139482	0.85[CEU][hapmap]
rs17418048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17418151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17418627	1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412634	1.00[JPT][hapmap]
rs4575120	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58623222	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6588567	0.85[CEU][hapmap]
rs6670673	0.85[CEU][hapmap]
rs6680818	0.85[CEU][hapmap]
rs6681925	0.85[CEU][hapmap]
rs6694786	0.92[CEU][hapmap]
rs7519540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548272	0.85[CEU][hapmap]
rs7549716	0.85[CEU][hapmap]
rs7550575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769989	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv526148	chr1:56101597-56146450	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56104600-56107200	Enhancers	NHEK	skin
2	chr1:56105000-56107400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:56105200-56107400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:56105800-56107400	Enhancers	Fetal Stomach	stomach
5	chr1:56106000-56107600	Enhancers	NHLF	lung
6	chr1:56106400-56107200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:56106400-56107400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:56106400-56107400	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:56106400-56107400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:56106600-56107200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:56106600-56107200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:56106600-56107200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr1:56106600-56107200	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr1:56106600-56107200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:56106600-56107200	Active TSS	Brain Substantia Nigra	brain
16	chr1:56106600-56107200	Active TSS	Duodenum Mucosa	Duodenum
17	chr1:56106600-56107200	Enhancers	Placenta	Placenta
18	chr1:56106600-56107200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr1:56106600-56107200	Active TSS	Right Atrium	heart
20	chr1:56106600-56107200	Active TSS	Thymus	Thymus
21	chr1:56106600-56107200	Flanking Active TSS	HUVEC	blood vessel
22	chr1:56106600-56107200	Flanking Active TSS	Osteobl	bone
23	chr1:56106600-56107400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:56106600-56107400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:56106600-56107400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:56106600-56107400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr1:56106600-56107400	Active TSS	Brain Angular Gyrus	brain
28	chr1:56106600-56107400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr1:56106600-56107400	Enhancers	Fetal Heart	heart
30	chr1:56106600-56107400	Enhancers	Fetal Kidney	kidney
31	chr1:56106600-56107400	Enhancers	Fetal Lung	lung
32	chr1:56106600-56107400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr1:56106600-56107400	Flanking Active TSS	HSMMtube	muscle
34	chr1:56106600-56107400	Flanking Active TSS	NHDF-Ad	bronchial
35	chr1:56106800-56107200	Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr1:56106800-56107200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr1:56106800-56107200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:56106800-56107200	Active TSS	Brain Hippocampus Middle	brain
39	chr1:56106800-56107200	Active TSS	Colon Smooth Muscle	Colon
40	chr1:56106800-56107200	Active TSS	Ovary	ovary
41	chr1:56106800-56107200	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:56106800-56107200	Active TSS	Rectal Smooth Muscle	rectum
43	chr1:56106800-56107200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:56106800-56107200	Flanking Active TSS	GM12878-XiMat	blood
45	chr1:56106800-56107200	Flanking Active TSS	HSMM	muscle
46	chr1:56106800-56107200	Enhancers	NH-A	brain
47	chr1:56106800-56107400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:56106800-56107400	Bivalent/Poised TSS	HepG2	liver
49	chr1:56107000-56107200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:56107000-56107200	Active TSS	Primary T cells fromperipheralblood	blood

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