Variant report

Variant	rs17005687
Chromosome Location	chr3:69413992-69413993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13320477	0.87[CHB][hapmap];0.82[EUR][1000 genomes]
rs17005675	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17005685	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17005689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005696	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17005699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005712	1.00[CEU][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17005713	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350402	0.93[CHB][hapmap];0.90[GIH][hapmap]
rs2314987	0.85[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2872808	0.84[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes]
rs4241387	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4855388	0.81[GIH][hapmap]
rs4855394	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5026329	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56653941	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56682655	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57343519	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58937767	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59683429	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60969945	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940765	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940769	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940771	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940775	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940779	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940783	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72940785	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881031	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs964553	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1800315	chr3:69374729-69414587	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv520818	chr3:69401248-69421495	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2760780	chr3:69413876-69513947	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:69403000-69414800	Weak transcription	Lung	lung
3	chr3:69410200-69417400	Weak transcription	Fetal Lung	lung
4	chr3:69412200-69415400	Enhancers	Dnd41	blood
5	chr3:69412800-69414000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr3:69412800-69414200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr3:69412800-69414600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:69412800-69415000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:69412800-69415200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:69413000-69414000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:69413000-69414000	Enhancers	Thymus	Thymus
12	chr3:69413000-69414400	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:69413000-69414600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:69413000-69414600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr3:69413000-69414800	Enhancers	GM12878-XiMat	blood
16	chr3:69413000-69414800	Enhancers	HMEC	breast
17	chr3:69413000-69415000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:69413000-69415000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:69413200-69414000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:69413200-69414000	Enhancers	Osteobl	bone
21	chr3:69413200-69414200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:69413400-69414000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:69413400-69414000	Flanking Active TSS	NHEK	skin
24	chr3:69413600-69415200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:69413600-69417200	Weak transcription	Aorta	Aorta
26	chr3:69413600-69417200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:69413600-69417200	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:69413600-69417200	Weak transcription	Fetal Thymus	thymus
29	chr3:69413600-69417400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:69413600-69417400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:69413600-69417400	Weak transcription	Brain Substantia Nigra	brain
32	chr3:69413600-69417600	Weak transcription	Esophagus	oesophagus
33	chr3:69413600-69418000	Weak transcription	HSMMtube	muscle
34	chr3:69413600-69419000	Weak transcription	NHDF-Ad	bronchial
35	chr3:69413800-69414000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:69413800-69414400	Enhancers	HSMM	muscle
37	chr3:69413800-69414600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:69413800-69417000	Weak transcription	HUVEC	blood vessel
39	chr3:69413800-69417400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:69413800-69417600	Weak transcription	Placenta	Placenta
41	chr3:69413800-69417600	Weak transcription	Right Atrium	heart
42	chr3:69413800-69419000	Weak transcription	Brain Angular Gyrus	brain
43	chr3:69413800-69419400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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