Variant report

Variant	rs62217194
Chromosome Location	chr20:25038372-25038373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25026036..25030944-chr20:25033529..25038477,7	MCF-7	breast:
2	chr20:24970831..24976063-chr20:25037253..25040567,5	MCF-7	breast:
3	chr20:24993232..24996113-chr20:25036389..25038769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1005409	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3646	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746331	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815365	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6076315	0.80[EUR][1000 genomes]
rs62217197	0.81[EUR][1000 genomes]
rs62217199	0.82[EUR][1000 genomes]
rs7265721	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265950	0.91[AMR][1000 genomes];0.92[EUR][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	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	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62217194	ENSG00000154930	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25036600-25038600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr20:25036600-25038600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr20:25036800-25038600	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr20:25036800-25038600	Flanking Bivalent TSS/Enh	HepG2	liver
5	chr20:25036800-25039200	Active TSS	Fetal Intestine Large	intestine
6	chr20:25037200-25038400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr20:25037200-25038600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:25037200-25038800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr20:25037200-25039800	Active TSS	Aorta	Aorta
10	chr20:25037400-25038600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr20:25037400-25038800	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
12	chr20:25037400-25039200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr20:25037400-25039200	Active TSS	Brain Angular Gyrus	brain
14	chr20:25037400-25039200	Active TSS	Fetal Intestine Small	intestine
15	chr20:25037400-25039400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr20:25037400-25039600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr20:25037400-25039600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr20:25037400-25039600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr20:25037400-25039600	Active TSS	Ovary	ovary
20	chr20:25037400-25040200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr20:25037600-25038400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr20:25037600-25038600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr20:25037600-25038600	Flanking Active TSS	HMEC	breast
24	chr20:25037600-25038600	Flanking Active TSS	HUVEC	blood vessel
25	chr20:25037600-25039000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:25037600-25039000	Active TSS	Primary T cells from cord blood	blood
27	chr20:25037600-25039000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr20:25037600-25039000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
29	chr20:25037600-25039000	Active TSS	Brain Cingulate Gyrus	brain
30	chr20:25037600-25039000	Active TSS	Brain Hippocampus Middle	brain
31	chr20:25037600-25039000	Active TSS	Stomach Mucosa	stomach
32	chr20:25037600-25039000	Active TSS	GM12878-XiMat	blood
33	chr20:25037600-25039200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr20:25037600-25039200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr20:25037600-25039200	Active TSS	Brain Anterior Caudate	brain
36	chr20:25037600-25039200	Active TSS	Fetal Lung	lung
37	chr20:25037600-25039200	Active TSS	Pancreas	Pancrea
38	chr20:25037600-25039200	Active TSS	Placenta Amnion	Placenta Amnion
39	chr20:25037600-25039200	Active TSS	Right Atrium	heart
40	chr20:25037600-25039200	Active TSS	A549	lung
41	chr20:25037600-25039400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
42	chr20:25037600-25039400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr20:25037600-25039400	Active TSS	Gastric	stomach
44	chr20:25037600-25039600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
45	chr20:25037600-25039600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
46	chr20:25037600-25039600	Active TSS	Colon Smooth Muscle	Colon
47	chr20:25037600-25039600	Active TSS	Left Ventricle	heart
48	chr20:25037600-25039600	Active TSS	Small Intestine	intestine
49	chr20:25037600-25039800	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr20:25037600-25039800	Active TSS	Fetal Kidney	kidney

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