Variant report

Variant	rs13409478
Chromosome Location	chr2:134081421-134081422
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	chr2:134073505..134075455-chr2:134080739..134083280,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10165601	0.93[CEU][hapmap];0.80[GIH][hapmap]
rs10175744	0.93[CEU][hapmap]
rs10180047	0.93[CEU][hapmap]
rs10182402	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10184630	0.93[CEU][hapmap]
rs10191826	0.91[ASW][hapmap];0.94[CEU][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10193087	0.92[CEU][hapmap]
rs12328723	0.93[CEU][hapmap]
rs12328976	0.81[CEU][hapmap]
rs12619465	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13400561	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13400743	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13406057	0.80[CEU][hapmap]
rs13406354	0.93[CEU][hapmap]
rs13407205	0.81[CEU][hapmap]
rs13407503	0.81[CEU][hapmap]
rs13411233	0.93[CEU][hapmap];0.80[GIH][hapmap]
rs13414823	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13432602	1.00[CEU][hapmap];0.85[GIH][hapmap];0.83[EUR][1000 genomes]
rs1346776	0.93[CEU][hapmap];0.85[GIH][hapmap]
rs1430165	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1430166	1.00[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs1430168	0.93[CEU][hapmap]
rs1435556	0.93[CEU][hapmap]
rs1435565	0.93[CEU][hapmap]
rs1435566	0.93[CEU][hapmap]
rs17802295	0.93[CEU][hapmap];0.80[GIH][hapmap]
rs2304404	0.87[CEU][hapmap]
rs56212259	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57942569	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58035542	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59037048	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62180011	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62180012	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6724854	0.97[ASN][1000 genomes]
rs6724865	0.96[ASN][1000 genomes]
rs9287426	0.93[CEU][hapmap];0.80[GIH][hapmap]
rs9808392	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834384	chr2:134005229-134188648	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1003964	chr2:134039363-134088319	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1014718	chr2:134067133-134151633	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134070200-134082200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:134070400-134094600	Weak transcription	NHEK	skin
3	chr2:134071200-134081600	Weak transcription	Right Ventricle	heart
4	chr2:134080600-134084600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:134081000-134084000	Enhancers	Hela-S3	cervix
6	chr2:134081000-134084200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:134081000-134085200	Weak transcription	Brain Anterior Caudate	brain
8	chr2:134081000-134087000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:134081200-134082800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:134081200-134083400	Enhancers	NHDF-Ad	bronchial
11	chr2:134081200-134083400	Enhancers	NHLF	lung
12	chr2:134081200-134085000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:134081200-134085000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:134081400-134081800	Flanking Active TSS	A549	lung
15	chr2:134081400-134084200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:134081400-134084800	Enhancers	Osteobl	bone

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