Variant report

Variant	rs2958079
Chromosome Location	chr3:111052780-111052781
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	chr3:111042529..111044033-chr3:111050844..111053535,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10511294	0.97[ASN][1000 genomes]
rs11920390	0.91[ASN][1000 genomes]
rs11920391	0.91[ASN][1000 genomes]
rs12106997	0.97[ASN][1000 genomes]
rs1489030	0.97[ASN][1000 genomes]
rs1489031	0.97[ASN][1000 genomes]
rs1489032	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489033	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1489034	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1489035	0.91[ASN][1000 genomes]
rs2634552	0.97[ASN][1000 genomes]
rs2634553	0.97[ASN][1000 genomes]
rs2634554	0.97[ASN][1000 genomes]
rs2675587	0.97[ASN][1000 genomes]
rs28831219	0.89[ASN][1000 genomes]
rs28846108	0.89[ASN][1000 genomes]
rs2932047	0.97[ASN][1000 genomes]
rs2932071	0.97[ASN][1000 genomes]
rs2932074	0.93[ASN][1000 genomes]
rs2950971	0.92[ASN][1000 genomes]
rs2958080	0.97[ASN][1000 genomes]
rs2971363	0.97[ASN][1000 genomes]
rs2971364	0.97[ASN][1000 genomes]
rs2971365	0.97[ASN][1000 genomes]
rs2971366	0.97[ASN][1000 genomes]
rs4145124	0.97[ASN][1000 genomes]
rs6808323	0.89[ASN][1000 genomes]
rs7620684	0.89[ASN][1000 genomes]
rs7621095	0.89[ASN][1000 genomes]
rs7624812	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636637	0.91[ASN][1000 genomes]
rs9837511	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9854335	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9868323	0.91[ASN][1000 genomes]
rs9878888	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv963486	chr3:111047149-111055574	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111045800-111054400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:111050800-111052800	Enhancers	Dnd41	blood
3	chr3:111051200-111052800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:111051400-111053200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr3:111051400-111053200	Enhancers	HSMMtube	muscle
6	chr3:111051600-111053200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:111051600-111053200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:111051600-111053200	Enhancers	HSMM	muscle
9	chr3:111051800-111053200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:111052000-111053800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:111052000-111054200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:111052000-111054400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:111052000-111054400	Weak transcription	Fetal Thymus	thymus
14	chr3:111052000-111054600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:111052000-111054800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:111052200-111053000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:111052200-111053200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:111052200-111053200	Enhancers	HMEC	breast
19	chr3:111052200-111053200	Enhancers	NHEK	skin
20	chr3:111052400-111053000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:111052400-111053000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:111052400-111053000	Enhancers	NH-A	brain
23	chr3:111052600-111052800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:111052600-111052800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:111052600-111053200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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