Variant report

Variant	rs62228516
Chromosome Location	chr3:25087193-25087194
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:25079124..25081667-chr3:25084641..25087586,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10510556	0.87[EUR][1000 genomes]
rs13327067	0.83[EUR][1000 genomes]
rs1603974	0.87[EUR][1000 genomes]
rs17515260	0.88[EUR][1000 genomes]
rs17515622	0.87[EUR][1000 genomes]
rs17787525	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17787531	0.88[EUR][1000 genomes]
rs62228512	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62228513	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62228518	0.87[EUR][1000 genomes]
rs62228519	0.87[EUR][1000 genomes]
rs62228520	0.87[EUR][1000 genomes]
rs62228521	0.87[EUR][1000 genomes]
rs62228538	0.87[EUR][1000 genomes]
rs62228539	0.85[EUR][1000 genomes]
rs62228543	0.80[EUR][1000 genomes]
rs7652292	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs949641	0.92[AMR][1000 genomes];1.00[EUR][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	nsv834644	chr3:24936987-25112610	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv589955	chr3:24987823-25113358	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25079400-25088400	Weak transcription	Adipose Nuclei	Adipose
2	chr3:25080000-25089000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:25083400-25087800	Enhancers	Fetal Heart	heart
4	chr3:25085600-25088200	Enhancers	Fetal Stomach	stomach
5	chr3:25085800-25088400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:25086000-25087600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:25086000-25087600	Enhancers	Stomach Smooth Muscle	stomach
8	chr3:25086000-25087800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:25086000-25087800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:25086200-25087600	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr3:25086200-25087800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:25086400-25087600	Enhancers	Rectal Smooth Muscle	rectum
13	chr3:25086400-25087800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:25086400-25087800	Enhancers	Fetal Lung	lung
15	chr3:25086600-25087200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:25086600-25087200	Enhancers	Colon Smooth Muscle	Colon
17	chr3:25086600-25087400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:25086600-25087600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:25086600-25087800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:25086600-25087800	Enhancers	Fetal Muscle Leg	muscle
21	chr3:25086600-25087800	Enhancers	Right Atrium	heart
22	chr3:25086600-25088200	Enhancers	Left Ventricle	heart
23	chr3:25086600-25088600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:25086800-25087200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:25086800-25087200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:25086800-25087200	Enhancers	Brain Germinal Matrix	brain
27	chr3:25086800-25087200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr3:25086800-25087200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:25086800-25087600	Enhancers	Aorta	Aorta
30	chr3:25086800-25087600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:25086800-25088400	Weak transcription	Fetal Intestine Small	intestine
32	chr3:25086800-25089000	Weak transcription	Right Ventricle	heart
33	chr3:25087000-25087400	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:25087000-25087600	Enhancers	Brain Angular Gyrus	brain
35	chr3:25087000-25087800	Enhancers	Brain Cingulate Gyrus	brain
36	chr3:25087000-25088000	Enhancers	Brain Anterior Caudate	brain
37	chr3:25087000-25089400	Enhancers	Brain Substantia Nigra	brain
38	chr3:25087000-25092600	Weak transcription	Fetal Kidney	kidney

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