Variant report

Variant	rs6014086
Chromosome Location	chr20:53239426-53239427
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52824416..52826891-chr20:53237816..53240042,2	MCF-7	breast:
2	chr20:53238514..53239494-chr8:126103691..126104564,2	MCF-7	breast:
3	chr20:52824772..52826427-chr20:53237648..53240107,2	MCF-7	breast:
4	chr20:53227273..53231686-chr20:53235441..53239585,4	MCF-7	breast:
5	chr20:53238250..53239788-chr20:53246518..53248056,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction
ENSG00000164961	Chromatin interaction
ENSG00000156831	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11906377	1.00[AMR][1000 genomes]
rs11908574	1.00[AMR][1000 genomes]
rs16999812	1.00[MEX][hapmap]
rs6014062	1.00[MEX][hapmap]
rs6023416	0.81[AFR][1000 genomes]
rs6023417	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6023419	0.88[AFR][1000 genomes]
rs6023427	0.91[ASW][hapmap];0.83[MKK][hapmap];1.00[AMR][1000 genomes]
rs6098050	1.00[MEX][hapmap]
rs6098052	1.00[MEX][hapmap]
rs6098058	1.00[MEX][hapmap]
rs6098076	1.00[MEX][hapmap]
rs6098078	1.00[MEX][hapmap]
rs6098079	1.00[MEX][hapmap]
rs6098081	1.00[MEX][hapmap]
rs6512962	1.00[MEX][hapmap]
rs7270950	1.00[MEX][hapmap]
rs73913626	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
2	chr20:53217400-53240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:53229200-53240600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr20:53235000-53241600	Enhancers	Fetal Brain Male	brain
5	chr20:53235200-53250400	Weak transcription	Psoas Muscle	Psoas
6	chr20:53236000-53241800	Weak transcription	Pancreas	Pancrea
7	chr20:53236200-53240600	Weak transcription	Right Atrium	heart
8	chr20:53236200-53240800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:53236200-53250400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr20:53236400-53240600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr20:53238200-53241000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr20:53238400-53240000	Enhancers	Brain Germinal Matrix	brain
13	chr20:53238400-53241000	Enhancers	Fetal Brain Female	brain
14	chr20:53238400-53242000	Enhancers	Fetal Muscle Trunk	muscle
15	chr20:53238400-53242800	Enhancers	Fetal Muscle Leg	muscle
16	chr20:53238600-53239600	Enhancers	Brain Anterior Caudate	brain
17	chr20:53238600-53242400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:53238800-53242400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr20:53238800-53242800	Enhancers	Fetal Lung	lung
20	chr20:53239000-53239600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:53239000-53239600	Enhancers	HSMMtube	muscle
22	chr20:53239000-53239600	Flanking Active TSS	NH-A	brain
23	chr20:53239000-53239600	Enhancers	Osteobl	bone
24	chr20:53239000-53239800	Enhancers	Brain Cingulate Gyrus	brain
25	chr20:53239000-53240000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr20:53239000-53240600	Enhancers	Brain Substantia Nigra	brain
27	chr20:53239000-53241000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr20:53239000-53241200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr20:53239200-53239600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:53239200-53240000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr20:53239200-53242000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:53239200-53242000	Enhancers	Brain Angular Gyrus	brain
33	chr20:53239400-53240400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr20:53239400-53240400	Weak transcription	Brain Hippocampus Middle	brain
35	chr20:53239400-53240400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr20:53239400-53240400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr20:53239400-53240600	Weak transcription	Fetal Heart	heart
38	chr20:53239400-53240600	Weak transcription	Fetal Stomach	stomach
39	chr20:53239400-53241400	Enhancers	NHDF-Ad	bronchial

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