Variant report

Variant	rs546942
Chromosome Location	chr15:53813328-53813329
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	chr15:53811069..53813390-chr15:53814144..53816117,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1009651	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10152470	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070986	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11630682	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11630747	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11856406	0.82[ASN][1000 genomes]
rs1516425	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17661801	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17712761	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1906414	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1906420	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1948128	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1962425	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2129772	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2171478	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414240	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414241	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28579287	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36074695	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4572330	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4776155	0.82[ASN][1000 genomes]
rs540546	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563716	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608518	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72745144	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041208	0.86[JPT][hapmap]
rs952993	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1040216	chr15:53743780-53851679	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv833009	chr15:53752901-53935303	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1038512	chr15:53803770-53851679	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53802000-53828000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:53804200-53821600	Weak transcription	A549	lung
3	chr15:53810000-53814200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:53810800-53817400	Strong transcription	Liver	Liver
5	chr15:53811000-53816200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:53812000-53816400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr15:53812600-53814600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:53812600-53815600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr15:53812600-53815800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:53813000-53813400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:53813200-53813400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:53813200-53813400	Active TSS	Brain Anterior Caudate	brain
13	chr15:53813200-53813400	Enhancers	Brain Hippocampus Middle	brain
14	chr15:53813200-53813400	Enhancers	Fetal Heart	heart
15	chr15:53813200-53813600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:53813200-53813600	Enhancers	Pancreas	Pancrea
17	chr15:53813200-53813800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:53813200-53814600	Enhancers	Brain Germinal Matrix	brain
19	chr15:53813200-53815600	Enhancers	Fetal Muscle Leg	muscle
20	chr15:53813200-53815600	Enhancers	HepG2	liver

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