Variant report

Variant	rs249721
Chromosome Location	chr5:115022257-115022258
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	chr5:115016498..115018135-chr5:115020605..115022466,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1067726	0.98[ASN][1000 genomes]
rs1067728	0.98[ASN][1000 genomes]
rs149472	0.87[ASN][1000 genomes]
rs152416	1.00[ASN][1000 genomes]
rs153073	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs153074	1.00[ASN][1000 genomes]
rs1651414	1.00[ASN][1000 genomes]
rs1698097	0.98[ASN][1000 genomes]
rs171662	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173733	0.91[ASN][1000 genomes]
rs2431441	0.91[ASN][1000 genomes]
rs2431443	0.91[ASN][1000 genomes]
rs2434727	0.91[ASN][1000 genomes]
rs2455447	0.91[ASN][1000 genomes]
rs2455450	0.91[ASN][1000 genomes]
rs249720	1.00[ASN][1000 genomes]
rs251878	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs251879	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2545847	0.93[ASN][1000 genomes]
rs2561860	0.98[ASN][1000 genomes]
rs2652663	0.96[ASN][1000 genomes]
rs3105151	0.96[ASN][1000 genomes]
rs397908	0.96[ASN][1000 genomes]
rs403039	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs422161	0.98[ASN][1000 genomes]
rs425666	0.98[ASN][1000 genomes]
rs432032	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs440138	0.98[ASN][1000 genomes]
rs440925	0.98[ASN][1000 genomes]
rs441398	0.98[ASN][1000 genomes]
rs447079	0.98[ASN][1000 genomes]
rs455226	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs459180	0.98[ASN][1000 genomes]
rs460451	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs461084	0.98[ASN][1000 genomes]
rs461105	0.93[ASN][1000 genomes]
rs461952	0.91[ASN][1000 genomes]
rs462799	0.98[ASN][1000 genomes]
rs465126	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs465457	0.91[ASN][1000 genomes]
rs465496	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs465997	0.94[ASN][1000 genomes]
rs712556	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733817	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs791565	1.00[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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 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	chr5:115020200-115022600	Enhancers	Brain Germinal Matrix	brain
2	chr5:115020400-115022600	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr5:115020400-115022600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr5:115020400-115022800	Enhancers	Fetal Lung	lung
5	chr5:115020600-115022800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:115020800-115022400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr5:115020800-115022800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:115021000-115022400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr5:115021200-115022400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:115021200-115022400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:115021200-115022400	Enhancers	Colon Smooth Muscle	Colon
12	chr5:115021200-115022400	Enhancers	Fetal Muscle Leg	muscle
13	chr5:115021200-115022600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:115021200-115022800	Enhancers	Adipose Nuclei	Adipose
15	chr5:115021400-115023000	Enhancers	Osteobl	bone
16	chr5:115021800-115022400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:115021800-115022400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:115021800-115022800	Enhancers	NH-A	brain
19	chr5:115022000-115022400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:115022000-115022600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:115022000-115022600	Enhancers	Ovary	ovary
22	chr5:115022200-115022600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:115022200-115022600	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr5:115022200-115022800	Enhancers	Aorta	Aorta
25	chr5:115022200-115022800	Bivalent Enhancer	NHDF-Ad	bronchial

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