Variant report

Variant	rs56012105
Chromosome Location	chr2:49080934-49080935
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:49080769..49083086-chr2:49086686..49089047,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10178052	0.82[ASN][1000 genomes]
rs10208693	0.82[ASN][1000 genomes]
rs11125184	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619514	0.84[ASN][1000 genomes]
rs12713015	0.82[ASN][1000 genomes]
rs12713017	0.87[ASN][1000 genomes]
rs12713018	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13016625	0.90[ASN][1000 genomes]
rs1558604	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17037739	0.81[ASN][1000 genomes]
rs4264602	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4290704	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4401253	0.90[ASN][1000 genomes]
rs4434043	0.91[ASN][1000 genomes]
rs4482537	0.90[ASN][1000 genomes]
rs4494801	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4621207	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4643585	0.97[AFR][1000 genomes]
rs6545074	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545075	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7567952	0.90[ASN][1000 genomes]
rs7603311	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv998864	chr2:49015878-49230000	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:49076000-49082800	Enhancers	HMEC	breast
2	chr2:49076400-49084800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:49076600-49081200	Enhancers	Osteobl	bone
4	chr2:49078200-49081400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:49078200-49081400	Enhancers	NHLF	lung
6	chr2:49079400-49082200	Weak transcription	NHEK	skin
7	chr2:49079600-49082200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:49079800-49081200	Enhancers	HSMM	muscle
9	chr2:49080200-49082200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:49080200-49083200	Enhancers	Stomach Smooth Muscle	stomach
11	chr2:49080400-49082200	Enhancers	HSMMtube	muscle
12	chr2:49080600-49081800	Weak transcription	Ovary	ovary
13	chr2:49080800-49081400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:49080800-49082000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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