Variant report

Variant	rs563819
Chromosome Location	chr13:30250724-30250725
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	chr13:30249644..30251920-chr13:30269289..30271724,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1023162	0.93[ASN][1000 genomes]
rs1023163	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1093774	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1104261	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12428341	0.96[ASN][1000 genomes]
rs17073936	1.00[CHB][hapmap]
rs182178	1.00[CHB][hapmap]
rs1886170	1.00[CHB][hapmap]
rs2089944	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2234417	1.00[CHB][hapmap]
rs2388240	0.90[ASN][1000 genomes]
rs2388243	0.84[ASN][1000 genomes]
rs2388244	1.00[CHB][hapmap]
rs2669033	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2776951	0.90[EUR][1000 genomes]
rs278037	1.00[CHB][hapmap]
rs280908	0.95[YRI][hapmap]
rs280920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280921	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280948	0.96[ASN][1000 genomes]
rs280957	0.93[ASN][1000 genomes]
rs280958	0.93[ASN][1000 genomes]
rs280959	0.96[ASN][1000 genomes]
rs280960	0.93[ASN][1000 genomes]
rs35803474	0.89[ASN][1000 genomes]
rs542930	0.89[ASN][1000 genomes]
rs547522	0.93[ASN][1000 genomes]
rs566688	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs573080	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs598281	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs630273	0.84[YRI][hapmap]
rs73157112	0.81[ASN][1000 genomes]
rs7326804	0.81[ASN][1000 genomes]
rs819102	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs819104	0.96[ASN][1000 genomes]
rs819406	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs819408	0.90[EUR][1000 genomes]
rs943564	0.90[ASN][1000 genomes]
rs9508556	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510577	chr13:30213612-30254316	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30248600-30252200	Enhancers	NHDF-Ad	bronchial
2	chr13:30249000-30251000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr13:30249200-30250800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr13:30249600-30252000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:30249800-30250800	Enhancers	HMEC	breast
6	chr13:30249800-30252000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr13:30249800-30252000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:30249800-30252000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr13:30249800-30252800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:30250000-30256400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr13:30250600-30250800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:30250600-30250800	Flanking Active TSS	Osteobl	bone
13	chr13:30250600-30251000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:30250600-30251000	Enhancers	Duodenum Mucosa	Duodenum
15	chr13:30250600-30251000	Enhancers	NH-A	brain
16	chr13:30250600-30251200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:30250600-30251200	Enhancers	Esophagus	oesophagus
18	chr13:30250600-30251200	Enhancers	Pancreas	Pancrea
19	chr13:30250600-30251400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:30250600-30251400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr13:30250600-30251400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr13:30250600-30251400	Enhancers	Hela-S3	cervix
23	chr13:30250600-30252000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr13:30250600-30252000	Flanking Active TSS	NHEK	skin

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