Variant report

Variant	rs2546960
Chromosome Location	chr5:167403035-167403036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10039736	0.86[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11134483	0.81[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap]
rs11134485	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs11955430	0.86[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12522181	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12523097	0.81[EUR][1000 genomes]
rs1345735	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17069646	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1821254	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1862419	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2546944	0.86[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2546957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2569047	0.86[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2617956	0.83[ASN][1000 genomes]
rs2617963	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2617981	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55859018	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6890434	0.91[CEU][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs730256	0.90[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs754925	0.81[CHB][hapmap]
rs889067	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs985650	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs992047	0.90[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830546	chr5:167303135-167456271	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167385800-167407400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:167388200-167407600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:167391600-167410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:167395200-167406800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:167396200-167407000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:167397000-167407800	Weak transcription	Left Ventricle	heart
7	chr5:167397200-167420800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:167400200-167405800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:167400800-167409400	Weak transcription	Right Ventricle	heart
10	chr5:167402200-167407200	Weak transcription	NHEK	skin
11	chr5:167402400-167404000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:167402400-167404600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:167402400-167407000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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