Variant report

Variant	rs6079058
Chromosome Location	chr20:13401065-13401066
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	chr20:13391938..13394510-chr20:13399097..13402083,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2057258	0.81[CHD][hapmap]
rs2070304	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273480	0.80[CHD][hapmap]
rs4814242	0.83[CHD][hapmap]
rs6074607	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6074619	0.92[ASN][1000 genomes]
rs6079065	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6079077	0.83[CHD][hapmap]
rs6079095	0.82[CHD][hapmap]
rs6079106	0.83[CEU][hapmap];0.83[CHD][hapmap];0.81[TSI][hapmap]
rs6109927	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6109958	0.83[CEU][hapmap]
rs6131476	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv21228	chr20:13283535-13447810	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1062049	chr20:13347580-13477455	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv544186	chr20:13347580-13477455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13364400-13415400	Weak transcription	Right Ventricle	heart
2	chr20:13364600-13416800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr20:13369000-13411200	Strong transcription	Dnd41	blood
4	chr20:13371400-13413600	Weak transcription	Ovary	ovary
5	chr20:13374200-13417200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:13374400-13410800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr20:13374600-13405800	Weak transcription	Fetal Stomach	stomach
8	chr20:13379000-13410200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr20:13379200-13463000	Weak transcription	HSMM	muscle
10	chr20:13390800-13403000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr20:13391200-13403400	Weak transcription	Fetal Kidney	kidney
12	chr20:13392600-13421400	Weak transcription	Psoas Muscle	Psoas
13	chr20:13392800-13415000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr20:13393800-13411000	Weak transcription	Pancreas	Pancrea
15	chr20:13393800-13416800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr20:13394000-13403000	Weak transcription	HMEC	breast
17	chr20:13394000-13415600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr20:13394200-13406800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:13394200-13416800	Weak transcription	Esophagus	oesophagus
20	chr20:13394200-13417200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr20:13395000-13415000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr20:13395400-13411000	Weak transcription	Spleen	Spleen
23	chr20:13395600-13416800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr20:13395600-13477800	Weak transcription	Gastric	stomach
25	chr20:13396000-13410600	Weak transcription	GM12878-XiMat	blood
26	chr20:13396000-13415000	Weak transcription	Brain Hippocampus Middle	brain
27	chr20:13396000-13417000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr20:13397400-13421200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr20:13397600-13410600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr20:13397800-13405400	Weak transcription	Fetal Lung	lung
31	chr20:13397800-13414400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr20:13397800-13415000	Weak transcription	Adipose Nuclei	Adipose
33	chr20:13398000-13403200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr20:13398000-13407400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr20:13398000-13410800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr20:13398000-13411000	Weak transcription	Primary B cells from cord blood	blood
37	chr20:13398200-13403000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr20:13398200-13403000	Weak transcription	NHEK	skin
39	chr20:13398200-13403600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr20:13398200-13404600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr20:13398200-13405400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr20:13398200-13406000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr20:13398200-13406000	Weak transcription	Fetal Muscle Leg	muscle
44	chr20:13398200-13406000	Weak transcription	Left Ventricle	heart
45	chr20:13398200-13409600	Weak transcription	Fetal Thymus	thymus
46	chr20:13398200-13410000	Weak transcription	Primary T cells from cord blood	blood
47	chr20:13398200-13410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr20:13398200-13410200	Weak transcription	Thymus	Thymus
49	chr20:13398200-13410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr20:13398200-13411000	Weak transcription	Lung	lung

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