Variant report

Variant	rs6050466
Chromosome Location	chr20:25210553-25210554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25209701-25211277	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr20:25210485-25210709	A549	lung:	n/a	n/a
3	TCF7L2	chr20:25210553-25211035	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25209487..25211779-chr20:25212504..25214793,2	MCF-7	breast:
2	chr20:25209268..25211969-chr20:25218955..25220793,2	MCF-7	breast:
3	chr20:25209269..25211589-chr20:25226481..25229322,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268302	TF binding region
ENSG00000100994	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs6050446	1.00[CHB][hapmap]
rs6115125	1.00[CHB][hapmap]
rs7273872	1.00[CHB][hapmap]

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:94 , 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	chr20:25193400-25210800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
4	chr20:25198400-25212200	Enhancers	Fetal Heart	heart
5	chr20:25199000-25212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr20:25199200-25210600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr20:25199200-25212000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr20:25199400-25210600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr20:25204200-25213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr20:25204400-25218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr20:25204800-25213600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr20:25206200-25211400	Enhancers	Right Atrium	heart
14	chr20:25206600-25214000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr20:25206800-25212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr20:25206800-25218200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr20:25207200-25210800	Enhancers	Right Ventricle	heart
18	chr20:25207200-25212600	Weak transcription	Brain Germinal Matrix	brain
19	chr20:25207200-25213800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr20:25207200-25213800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr20:25207400-25211000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr20:25207400-25213200	Weak transcription	Fetal Thymus	thymus
23	chr20:25207800-25210600	Weak transcription	Aorta	Aorta
24	chr20:25207800-25218200	Weak transcription	Spleen	Spleen
25	chr20:25207800-25218200	Weak transcription	Dnd41	blood
26	chr20:25208000-25210600	Weak transcription	Fetal Stomach	stomach
27	chr20:25208000-25212200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr20:25208000-25212600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr20:25208400-25210600	Weak transcription	Thymus	Thymus
30	chr20:25208400-25212200	Weak transcription	Primary T cells from cord blood	blood
31	chr20:25208400-25213400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:25208400-25213600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr20:25208400-25214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr20:25208400-25214000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr20:25208400-25214000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr20:25208400-25214000	Weak transcription	Placenta	Placenta
37	chr20:25208400-25214200	Weak transcription	Brain Substantia Nigra	brain
38	chr20:25208600-25210600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr20:25208600-25210600	Weak transcription	Adipose Nuclei	Adipose
40	chr20:25208600-25210600	Weak transcription	Colonic Mucosa	Colon
41	chr20:25208600-25210600	Weak transcription	Gastric	stomach
42	chr20:25208600-25210600	Weak transcription	HUVEC	blood vessel
43	chr20:25208600-25210600	Weak transcription	K562	blood
44	chr20:25208600-25211800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr20:25208600-25211800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr20:25208600-25213200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:25208600-25213200	Weak transcription	Hela-S3	cervix
48	chr20:25208600-25213400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr20:25208600-25213400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr20:25208600-25213400	Weak transcription	Ovary	ovary

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