Variant report

Variant	rs2278516
Chromosome Location	chr3:53807148-53807149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53741820..53744207-chr3:53806615..53808159,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11707420	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1829423	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2278517	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2278518	0.81[CEU][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs2612027	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2680650	0.87[CHB][hapmap];0.89[EUR][1000 genomes]
rs3774572	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3774579	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs3774586	0.83[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes]
rs3774589	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3774591	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3821865	0.91[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687740	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617553	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9881910	0.95[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
2	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine
3	chr3:53781800-53807400	Weak transcription	Brain Anterior Caudate	brain
4	chr3:53785000-53811200	Weak transcription	Spleen	Spleen
5	chr3:53786000-53808200	Weak transcription	Liver	Liver
6	chr3:53789800-53814600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:53796800-53808000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:53798000-53807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:53798800-53807400	Weak transcription	Fetal Brain Male	brain
10	chr3:53802000-53807400	Strong transcription	Fetal Lung	lung
11	chr3:53802200-53807200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:53802400-53818200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:53803000-53807400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:53803400-53808200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:53803600-53807400	Weak transcription	Lung	lung
16	chr3:53803800-53807400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:53803800-53808000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:53805000-53810200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:53805200-53807400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:53805200-53807400	Weak transcription	Pancreas	Pancrea
21	chr3:53806000-53807800	Enhancers	GM12878-XiMat	blood
22	chr3:53806200-53811800	Enhancers	NHDF-Ad	bronchial
23	chr3:53806400-53808200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:53806400-53808600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:53806600-53807400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:53806600-53808200	Enhancers	Fetal Stomach	stomach
27	chr3:53806600-53808400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:53806600-53808400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:53806600-53808400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:53806600-53808800	Enhancers	NHLF	lung
31	chr3:53806800-53807600	Enhancers	Brain Angular Gyrus	brain
32	chr3:53806800-53807600	Enhancers	Placenta	Placenta
33	chr3:53806800-53807600	Enhancers	Right Atrium	heart
34	chr3:53806800-53808000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:53806800-53808000	Enhancers	Fetal Muscle Leg	muscle
36	chr3:53806800-53808400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:53806800-53808400	Enhancers	Adipose Nuclei	Adipose
38	chr3:53806800-53808400	Enhancers	Osteobl	bone
39	chr3:53806800-53813000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:53807000-53807400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:53807000-53807600	Enhancers	Fetal Muscle Trunk	muscle
42	chr3:53807000-53807800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:53807000-53807800	Bivalent Enhancer	HSMMtube	muscle
44	chr3:53807000-53808200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:53807000-53808200	Enhancers	Fetal Brain Female	brain
46	chr3:53807000-53808400	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr3:53807000-53808400	Enhancers	Ovary	ovary
48	chr3:53807000-53808600	Enhancers	Fetal Thymus	thymus
49	chr3:53807000-53808800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:53807000-53809000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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