Variant report

Variant	rs35380838
Chromosome Location	chr5:125035754-125035755
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:125033776..125036628-chr5:125040323..125041930,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11950923	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11954141	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11955142	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11955150	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1490976	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1490981	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17153120	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17153142	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17153195	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17153198	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2101603	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28684625	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34407148	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35762924	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62385960	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62385965	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62385966	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62385967	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66490821	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6865600	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6883544	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7707067	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7723274	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs902593	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs989983	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	nsv534468	chr5:124943170-125634960	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:125021800-125055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:125033200-125035800	Weak transcription	NH-A	brain
3	chr5:125033200-125036200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:125033400-125036200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:125033400-125039200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:125034200-125037000	Enhancers	Fetal Kidney	kidney
7	chr5:125034600-125036000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:125035200-125036600	Enhancers	HSMM	muscle
9	chr5:125035200-125036800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:125035200-125037000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:125035200-125037000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:125035200-125037000	Enhancers	Stomach Mucosa	stomach
13	chr5:125035400-125036000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:125035400-125036000	Enhancers	Liver	Liver
15	chr5:125035400-125036400	Enhancers	HepG2	liver
16	chr5:125035600-125035800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:125035600-125035800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:125035600-125035800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr5:125035600-125035800	Flanking Active TSS	NHDF-Ad	bronchial
20	chr5:125035600-125036000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:125035600-125036000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:125035600-125036000	Enhancers	Adipose Nuclei	Adipose
23	chr5:125035600-125036000	Enhancers	Brain Anterior Caudate	brain
24	chr5:125035600-125036000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr5:125035600-125036000	Enhancers	Fetal Intestine Large	intestine
26	chr5:125035600-125036000	Enhancers	Fetal Lung	lung
27	chr5:125035600-125036000	Enhancers	Pancreas	Pancrea
28	chr5:125035600-125036000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr5:125035600-125036000	Enhancers	Osteobl	bone
30	chr5:125035600-125036200	Enhancers	Fetal Intestine Small	intestine
31	chr5:125035600-125036200	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr5:125035600-125036200	Enhancers	HSMMtube	muscle
33	chr5:125035600-125036400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr5:125035600-125036400	Enhancers	Brain Germinal Matrix	brain
35	chr5:125035600-125036400	Enhancers	Fetal Brain Male	brain
36	chr5:125035600-125036600	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr5:125035600-125036600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:125035600-125036600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:125035600-125036600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr5:125035600-125036600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:125035600-125036600	Enhancers	Fetal Muscle Leg	muscle
42	chr5:125035600-125036600	Enhancers	Fetal Stomach	stomach
43	chr5:125035600-125036600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr5:125035600-125036600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr5:125035600-125036600	Active TSS	A549	lung

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