Variant report

Variant	rs6050467
Chromosome Location	chr20:25212172-25212173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25210678..25212616-chr20:25212688..25215321,2	MCF-7	breast:
2	chr20:24972110..24973767-chr20:25211986..25214800,2	MCF-7	breast:
3	chr20:25210927..25216331-chr20:25216727..25222043,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs55879612	1.00[AMR][1000 genomes]
rs56063344	1.00[AMR][1000 genomes]
rs56343188	1.00[AMR][1000 genomes]
rs56374952	1.00[AMR][1000 genomes]
rs57359365	1.00[AMR][1000 genomes]
rs57509861	1.00[AMR][1000 genomes]
rs58134777	1.00[AMR][1000 genomes]
rs6037066	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6050480	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61245897	1.00[AMR][1000 genomes]
rs73904004	1.00[AMR][1000 genomes]
rs73904009	1.00[AMR][1000 genomes]
rs73904014	1.00[AMR][1000 genomes]
rs73904015	1.00[AMR][1000 genomes]
rs73904016	1.00[AMR][1000 genomes]
rs73904018	1.00[AMR][1000 genomes]
rs73904030	1.00[AMR][1000 genomes]
rs73904034	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73904035	1.00[AMR][1000 genomes]
rs73904040	1.00[AMR][1000 genomes]
rs73904467	1.00[AMR][1000 genomes]
rs73904468	1.00[AMR][1000 genomes]
rs73904472	1.00[AMR][1000 genomes]
rs73906090	1.00[AMR][1000 genomes]
rs73907308	1.00[AMR][1000 genomes]
rs73907312	1.00[AMR][1000 genomes]
rs73907315	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
3	chr20:25198400-25212200	Enhancers	Fetal Heart	heart
4	chr20:25199000-25212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr20:25204200-25213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr20:25204400-25218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr20:25204800-25213600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr20:25206600-25214000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr20:25206800-25212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr20:25206800-25218200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr20:25207200-25212600	Weak transcription	Brain Germinal Matrix	brain
13	chr20:25207200-25213800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr20:25207200-25213800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr20:25207400-25213200	Weak transcription	Fetal Thymus	thymus
16	chr20:25207800-25218200	Weak transcription	Spleen	Spleen
17	chr20:25207800-25218200	Weak transcription	Dnd41	blood
18	chr20:25208000-25212200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr20:25208000-25212600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr20:25208400-25212200	Weak transcription	Primary T cells from cord blood	blood
21	chr20:25208400-25213400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr20:25208400-25213600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr20:25208400-25214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr20:25208400-25214000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr20:25208400-25214000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr20:25208400-25214000	Weak transcription	Placenta	Placenta
27	chr20:25208400-25214200	Weak transcription	Brain Substantia Nigra	brain
28	chr20:25208600-25213200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:25208600-25213200	Weak transcription	Hela-S3	cervix
30	chr20:25208600-25213400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr20:25208600-25213400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr20:25208600-25213400	Weak transcription	Ovary	ovary
33	chr20:25208600-25213400	Weak transcription	HMEC	breast
34	chr20:25208600-25213400	Weak transcription	Osteobl	bone
35	chr20:25208600-25213600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr20:25208600-25213600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:25208600-25213600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr20:25208600-25213600	Weak transcription	Liver	Liver
39	chr20:25208600-25213800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr20:25208600-25213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr20:25208600-25213800	Weak transcription	Esophagus	oesophagus
42	chr20:25208600-25213800	Weak transcription	Fetal Intestine Large	intestine
43	chr20:25208600-25213800	Weak transcription	HSMM	muscle
44	chr20:25208600-25213800	Weak transcription	HSMMtube	muscle
45	chr20:25208600-25213800	Weak transcription	NHLF	lung
46	chr20:25208600-25214000	Weak transcription	Psoas Muscle	Psoas
47	chr20:25208600-25218200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr20:25208800-25213400	Weak transcription	NH-A	brain
49	chr20:25208800-25213800	Weak transcription	NHDF-Ad	bronchial
50	chr20:25209200-25218200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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