Variant report

Variant	rs9877603
Chromosome Location	chr3:78888961-78888962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78887158..78889804-chr3:78895316..78898187,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11127634	0.83[ASN][1000 genomes]
rs1480687	0.96[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs1480688	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1487139	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs162870	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1840969	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs1843786	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28629289	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs333491	0.94[JPT][hapmap]
rs333495	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs416551	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs439325	0.81[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs444598	0.84[CHB][hapmap];1.00[YRI][hapmap]
rs510006	0.83[CHB][hapmap]
rs9309819	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9309820	0.96[CEU][hapmap]
rs967454	1.00[YRI][hapmap]
rs9835958	0.92[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs9837982	0.88[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9861264	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9863758	0.84[CEU][hapmap]
rs9873248	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9875094	1.00[YRI][hapmap]
rs9881587	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78882000-78894800	Weak transcription	Fetal Intestine Small	intestine
2	chr3:78886200-78895800	Weak transcription	NHLF	lung
3	chr3:78887200-78893000	Enhancers	HepG2	liver
4	chr3:78887400-78889400	Enhancers	Hela-S3	cervix
5	chr3:78887800-78889400	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr3:78887800-78896000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:78888800-78889000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:78888800-78889000	Enhancers	Fetal Lung	lung
9	chr3:78888800-78889200	Active TSS	A549	lung
10	chr3:78888800-78889400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:78888800-78889400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:78888800-78889400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:78888800-78889400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:78888800-78889400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:78888800-78889400	Enhancers	Brain Angular Gyrus	brain
16	chr3:78888800-78889400	Enhancers	Brain Hippocampus Middle	brain
17	chr3:78888800-78889400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:78888800-78889400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:78888800-78889400	Enhancers	HSMM	muscle
20	chr3:78888800-78889400	Enhancers	HUVEC	blood vessel
21	chr3:78888800-78889400	Enhancers	NH-A	brain
22	chr3:78888800-78889400	Enhancers	NHDF-Ad	bronchial
23	chr3:78888800-78889400	Enhancers	Osteobl	bone
24	chr3:78888800-78889600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:78888800-78889800	Enhancers	Brain Substantia Nigra	brain

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