Variant report

Variant	rs62215277
Chromosome Location	chr20:25064864-25064865
allele	A/G
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	CTCF	chr20:25064780-25064930	AoAF	blood vessel:	n/a	n/a
2	SUZ12	chr20:25061549-25065864	NT2-D1	testis:	n/a	n/a
3	POLR2A	chr20:25064831-25064864	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr20:25064083-25065434	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTBP2	chr20:25064402-25065179	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25058531..25060558-chr20:25063145..25065745,2	MCF-7	breast:

Variant related genes	Relation type
VSX1	TF binding region
ENSG00000100987	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005409	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[ASN][1000 genomes]
rs2387577	1.00[ASN][1000 genomes]
rs4813546	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815366	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037014	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083736	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083737	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.84[ASN][1000 genomes]
rs6115024	1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217195	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217196	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217197	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217199	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7263632	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265721	0.80[EUR][1000 genomes]
rs7266451	1.00[ASN][1000 genomes]
rs7344824	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25061800-25065800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr20:25061800-25065800	Bivalent Enhancer	Fetal Brain Male	brain
3	chr20:25061800-25065800	Enhancers	Pancreas	Pancrea
4	chr20:25063400-25065000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr20:25063600-25065400	Bivalent Enhancer	Fetal Heart	heart
6	chr20:25063600-25065800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr20:25063800-25065200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr20:25063800-25065200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:25063800-25065200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr20:25063800-25065200	Bivalent Enhancer	Liver	Liver
11	chr20:25063800-25065200	Bivalent Enhancer	Esophagus	oesophagus
12	chr20:25063800-25065400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr20:25063800-25065400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
14	chr20:25063800-25065400	Bivalent Enhancer	Left Ventricle	heart
15	chr20:25063800-25065600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr20:25063800-25065600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
17	chr20:25063800-25065800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr20:25063800-25065800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr20:25063800-25065800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr20:25063800-25065800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
21	chr20:25063800-25066000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
22	chr20:25063800-25066400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr20:25064000-25065000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
24	chr20:25064000-25065000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
25	chr20:25064000-25065000	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr20:25064000-25065200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
27	chr20:25064000-25065400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
28	chr20:25064000-25065400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
29	chr20:25064000-25065600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
30	chr20:25064000-25065600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
31	chr20:25064000-25065600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
32	chr20:25064000-25065800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr20:25064000-25065800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr20:25064000-25065800	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr20:25064000-25066000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
36	chr20:25064200-25065000	Active TSS	Right Ventricle	heart
37	chr20:25064200-25065200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr20:25064200-25065200	Bivalent/Poised TSS	A549	lung
39	chr20:25064200-25065400	Bivalent Enhancer	Colon Smooth Muscle	Colon
40	chr20:25064200-25065400	Flanking Bivalent TSS/Enh	Dnd41	blood
41	chr20:25064200-25065600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
42	chr20:25064400-25065000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
43	chr20:25064400-25065000	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr20:25064400-25065000	Enhancers	Right Atrium	heart
45	chr20:25064400-25065000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
46	chr20:25064400-25065600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25064400-25065600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
48	chr20:25064400-25065800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr20:25064400-25065800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
50	chr20:25064600-25065000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell

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