Variant report

Variant	rs1409860
Chromosome Location	chr20:10904550-10904551
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:10651926..10653602-chr20:10903753..10905661,2	MCF-7	breast:
2	chr20:10652269..10654577-chr20:10901037..10905418,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270792	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4142362	0.82[EUR][1000 genomes]
rs6077958	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6077959	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6077961	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7268812	0.80[ASN][1000 genomes]
rs73604346	0.95[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	nsv1065969	chr20:10850562-11464172	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv544181	chr20:10850562-11464172	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv912663	chr20:10891798-10963675	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2758513	chr20:10892138-11116725	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv2758781	chr20:10892138-11116725	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:10891800-10904800	Weak transcription	Lung	lung
2	chr20:10899600-10906400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr20:10900000-10906800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:10900000-10906800	Enhancers	HMEC	breast
5	chr20:10900600-10908000	Weak transcription	Right Atrium	heart
6	chr20:10900800-10905800	Weak transcription	Spleen	Spleen
7	chr20:10901000-10907800	Weak transcription	Ovary	ovary
8	chr20:10901000-10920200	Weak transcription	Aorta	Aorta
9	chr20:10901200-10907000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:10902600-10905000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:10902600-10906000	Enhancers	Fetal Lung	lung
12	chr20:10902600-10906800	Enhancers	NHLF	lung
13	chr20:10902800-10905800	Enhancers	HSMM	muscle
14	chr20:10902800-10906200	Enhancers	Fetal Stomach	stomach
15	chr20:10903000-10906800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr20:10903200-10906200	Enhancers	HSMMtube	muscle
17	chr20:10903200-10906400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr20:10903200-10906800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr20:10903400-10904600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr20:10903600-10905000	Weak transcription	Small Intestine	intestine
21	chr20:10903800-10905200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr20:10903800-10905600	Enhancers	NHEK	skin
23	chr20:10903800-10906200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:10903800-10906800	Enhancers	NHDF-Ad	bronchial
25	chr20:10903800-10907400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr20:10904000-10905000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr20:10904000-10905400	Weak transcription	Pancreas	Pancrea
28	chr20:10904000-10906000	Enhancers	Hela-S3	cervix
29	chr20:10904000-10909400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr20:10904200-10905000	Weak transcription	NH-A	brain
31	chr20:10904200-10906000	Weak transcription	Placenta	Placenta
32	chr20:10904200-10906200	Enhancers	A549	lung
33	chr20:10904200-10906800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr20:10904200-10906800	Enhancers	Osteobl	bone
35	chr20:10904200-10909000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr20:10904200-10909000	Weak transcription	Adipose Nuclei	Adipose
37	chr20:10904200-10909200	Weak transcription	Fetal Muscle Leg	muscle
38	chr20:10904200-10909400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr20:10904400-10904800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr20:10904400-10904800	Weak transcription	HUVEC	blood vessel

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