Variant report

Variant	rs2872808
Chromosome Location	chr3:69409605-69409606
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12635365	0.86[ASN][1000 genomes]
rs13320477	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17005675	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[AMR][1000 genomes]
rs17005685	0.84[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes]
rs17005687	0.84[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes]
rs17005689	0.89[AMR][1000 genomes]
rs17005691	0.85[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes]
rs17005694	0.84[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes]
rs17005696	0.93[AMR][1000 genomes]
rs17005699	0.84[CEU][hapmap];0.87[CHB][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17005712	0.85[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17005713	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17350402	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17416638	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2314987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35298402	0.86[ASN][1000 genomes]
rs4241387	0.85[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4855388	0.82[CHB][hapmap]
rs4855391	0.85[ASN][1000 genomes]
rs4855394	0.82[CEU][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs5026329	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56052332	0.82[ASN][1000 genomes]
rs56138041	0.82[ASN][1000 genomes]
rs56653941	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs56682655	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs57343519	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs58156018	0.85[ASN][1000 genomes]
rs58937767	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs59605214	0.85[ASN][1000 genomes]
rs59683429	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs60969945	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72940765	0.80[AMR][1000 genomes]
rs72940769	0.87[AMR][1000 genomes]
rs72940771	0.85[AMR][1000 genomes]
rs72940775	0.85[AMR][1000 genomes]
rs72940779	0.85[AMR][1000 genomes]
rs72940783	0.87[AMR][1000 genomes]
rs72940785	0.85[AMR][1000 genomes]
rs881031	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs964553	0.85[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][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	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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69400600-69412800	Weak transcription	Esophagus	oesophagus
2	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:69402800-69413000	Weak transcription	Aorta	Aorta
4	chr3:69403000-69414800	Weak transcription	Lung	lung
5	chr3:69403800-69413000	Weak transcription	Thymus	Thymus
6	chr3:69406600-69412800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:69406800-69413000	Weak transcription	Brain Substantia Nigra	brain
8	chr3:69406800-69413400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:69407000-69412800	Weak transcription	HSMM	muscle
10	chr3:69407400-69412800	Weak transcription	NHEK	skin
11	chr3:69407400-69413200	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:69407600-69413000	Weak transcription	HMEC	breast
13	chr3:69408200-69409800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:69408400-69412800	Weak transcription	Fetal Thymus	thymus
15	chr3:69408600-69410000	Enhancers	HUVEC	blood vessel
16	chr3:69408600-69410800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:69408600-69413000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:69408600-69413000	Weak transcription	HSMMtube	muscle
19	chr3:69408800-69412800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:69409000-69409800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:69409000-69410000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:69409000-69411200	Enhancers	Dnd41	blood
23	chr3:69409200-69409800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr3:69409400-69413000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:69409600-69409800	Enhancers	Brain Cingulate Gyrus	brain
26	chr3:69409600-69410200	Enhancers	Fetal Lung	lung

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