Variant report

Variant	rs2046908
Chromosome Location	chr5:124817800-124817801
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	chr5:124816573..124819551-chr5:124822797..124825714,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10076405	0.85[ASN][1000 genomes]
rs11241809	0.83[ASN][1000 genomes]
rs1388215	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1400870	0.88[ASN][1000 genomes]
rs1400872	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1491066	0.82[ASN][1000 genomes]
rs2056216	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130845	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4407631	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4425501	0.86[ASN][1000 genomes]
rs4466164	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4621558	0.83[ASN][1000 genomes]
rs6595616	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6862357	0.89[ASN][1000 genomes]
rs6875072	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6876182	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6895537	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724863	0.89[ASN][1000 genomes]
rs769334	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs968759	0.91[ASN][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	nsv1030992	chr5:124708549-125391503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv537892	chr5:124708549-125391503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv882824	chr5:124789500-124875058	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124813400-124819400	Weak transcription	Stomach Mucosa	stomach
2	chr5:124813600-124819000	Weak transcription	HSMMtube	muscle
3	chr5:124813600-124819200	Weak transcription	HMEC	breast
4	chr5:124813600-124819400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:124813600-124819400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:124813600-124819400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:124814000-124819200	Weak transcription	HUVEC	blood vessel
8	chr5:124814600-124819400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:124814600-124819400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:124814600-124819400	Weak transcription	NHEK	skin
11	chr5:124814600-124819800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:124814800-124819600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:124815000-124819800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr5:124815800-124821600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:124816200-124818200	Enhancers	NHDF-Ad	bronchial
16	chr5:124816400-124817800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:124816400-124818000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:124816400-124822600	Enhancers	Fetal Brain Male	brain
19	chr5:124816600-124817800	Enhancers	Brain Anterior Caudate	brain
20	chr5:124816600-124817800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr5:124816600-124818000	Enhancers	Brain Hippocampus Middle	brain
22	chr5:124816600-124818400	Enhancers	Fetal Brain Female	brain
23	chr5:124816800-124817800	Enhancers	Brain Angular Gyrus	brain
24	chr5:124816800-124817800	Enhancers	Brain Substantia Nigra	brain
25	chr5:124816800-124818000	Enhancers	Brain Cingulate Gyrus	brain
26	chr5:124816800-124818000	Enhancers	Fetal Stomach	stomach
27	chr5:124816800-124818000	Enhancers	Rectal Smooth Muscle	rectum
28	chr5:124817000-124818000	Enhancers	Colon Smooth Muscle	Colon
29	chr5:124817000-124819400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:124817000-124819600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:124817200-124817800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:124817200-124817800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:124817400-124817800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:124817400-124817800	Enhancers	Fetal Lung	lung
35	chr5:124817400-124819400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:124817600-124817800	Enhancers	Aorta	Aorta
37	chr5:124817600-124817800	Enhancers	Brain Germinal Matrix	brain
38	chr5:124817600-124817800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr5:124817600-124820000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr5:124817800-124818000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:124817800-124818000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:124817800-124818800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:124817800-124819000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:124817800-124819400	Weak transcription	Brain Angular Gyrus	brain
45	chr5:124817800-124819400	Weak transcription	Brain Anterior Caudate	brain
46	chr5:124817800-124819400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:124817800-124819400	Weak transcription	Brain Substantia Nigra	brain
48	chr5:124817800-124819600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:124817800-124819600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:124817800-124820000	Weak transcription	Fetal Lung	lung

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