Variant report

Variant	rs6083739
Chromosome Location	chr20:25063832-25063833
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr20:25061549-25065864	NT2-D1	testis:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:25063817-25063867	HAEpiC	amniotic membrane:	n/a
2	chr20:25063817-25063867	NB4	blood:	n/a
3	chr20:25063817-25063867	HEEpiC	esophagus:	n/a
4	chr20:25063817-25063867	Hela-S3	cervix:	n/a
5	chr20:25063817-25063867	AG09309	skin:	n/a
6	chr20:25063817-25063867	BE2_C	brain:	n/a
7	chr20:25063817-25063867	AG09319	gingival:	n/a
8	chr20:25063817-25063867	HCF	heart:	n/a
9	chr20:25063817-25063867	H1-hESC	embryonic stem cell:	embryo
10	chr20:25063817-25063867	AG10803	skin:	n/a
11	chr20:25063817-25063867	HIPEpiC	eye:	n/a
12	chr20:25063817-25063867	Jurkat	blood:	n/a
13	chr20:25063817-25063867	SK-N-MC	brain:	n/a
14	chr20:25063817-25063867	ovcar-3	ovarian:	n/a
15	chr20:25063817-25063867	NH-A	brain:	n/a
16	chr20:25063817-25063867	Hepatocyte	liver:	n/a
17	chr20:25063817-25063867	GM12878	blood:	n/a
18	chr20:25063817-25063867	AG04449	skin:	fetal
19	chr20:25063817-25063867	PrEC	prostate:	n/a
20	chr20:25063817-25063867	AoSMC	blood vessel:	n/a
21	chr20:25063817-25063867	ProgFib	skin:	n/a
22	chr20:25063817-25063867	HMEC	breast:	n/a
23	chr20:25063817-25063867	U87	brain:	n/a
24	chr20:25063817-25063867	NT2-D1	testis:	n/a
25	chr20:25063817-25063867	GM12891	blood:	n/a
26	chr20:25063817-25063867	HRCEpiC	kidney:	n/a
27	chr20:25063817-25063867	PANC-1	pancreas:	n/a
28	chr20:25063817-25063867	SAEC	small airway:	n/a
29	chr20:25063817-25063867	MCF10A-Er-Src	breast:	n/a
30	chr20:25063817-25063867	NHDF-neo	bronchial:	n/a
31	chr20:25063817-25063867	T-47D	breast:	n/a
32	chr20:25063817-25063867	PFSK-1	brain:	n/a
33	chr20:25063817-25063867	SK-N-SH_RA	brain:	n/a
34	chr20:25063817-25063867	GM19239	blood:	n/a
35	chr20:25063817-25063867	GM06990	blood:	n/a
36	chr20:25063817-25063867	SK-N-SH	brain:	n/a
37	chr20:25063817-25063867	HL-60	blood:	n/a
38	chr20:25063817-25063867	NHBE	bronchial:	n/a
39	chr20:25063817-25063867	A549	lung:	n/a
40	chr20:25063817-25063867	SKMC	muscle:	n/a
41	chr20:25063817-25063867	MCF-7	breast:	n/a
42	chr20:25063817-25063867	IMR90	lung:	fetal
43	chr20:25063817-25063867	ECC-1	luminal epithelium:	n/a
44	chr20:25063817-25063867	HNPCEpiC	eye:	n/a
45	chr20:25063817-25063867	GM12892	blood:	n/a
46	chr20:25063817-25063867	HCT-116	colon:	n/a
47	chr20:25063817-25063867	K562	blood:	n/a
48	chr20:25063817-25063867	Caco-2	colon:	n/a
49	chr20:25063817-25063867	LNCaP	prostate:	n/a
50	chr20:25063817-25063867	HUVEC	blood vessel:	n/a

(count:1 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1005409	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2387577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4813546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037013	1.00[JPT][hapmap]
rs6037014	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[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	1.00[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[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.88[AFR][1000 genomes];1.00[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265721	0.80[EUR][1000 genomes]
rs7266451	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7344824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.81[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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25061600-25064600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
2	chr20:25061800-25064000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr20:25061800-25064000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
4	chr20:25061800-25065800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr20:25061800-25065800	Bivalent Enhancer	Fetal Brain Male	brain
6	chr20:25061800-25065800	Enhancers	Pancreas	Pancrea
7	chr20:25062400-25064000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
8	chr20:25062400-25064200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
9	chr20:25062800-25064600	Weak transcription	Gastric	stomach
10	chr20:25063200-25064400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr20:25063400-25064600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
12	chr20:25063400-25065000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
13	chr20:25063600-25064000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr20:25063600-25064000	Bivalent/Poised TSS	Fetal Brain Female	brain
15	chr20:25063600-25064400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr20:25063600-25065400	Bivalent Enhancer	Fetal Heart	heart
17	chr20:25063600-25065800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr20:25063800-25064000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:25063800-25064000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:25063800-25064000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr20:25063800-25064000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr20:25063800-25064000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr20:25063800-25064000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
24	chr20:25063800-25064000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
25	chr20:25063800-25064000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
26	chr20:25063800-25064000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
27	chr20:25063800-25064000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr20:25063800-25064000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
29	chr20:25063800-25064000	Bivalent Enhancer	Brain Anterior Caudate	brain
30	chr20:25063800-25064000	Bivalent Enhancer	Ovary	ovary
31	chr20:25063800-25064000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
32	chr20:25063800-25064000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr20:25063800-25064000	Flanking Bivalent TSS/Enh	NHEK	skin
34	chr20:25063800-25064200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
35	chr20:25063800-25064200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr20:25063800-25064200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
37	chr20:25063800-25064200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr20:25063800-25064200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr20:25063800-25064200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
40	chr20:25063800-25064400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr20:25063800-25064400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr20:25063800-25064400	Bivalent Enhancer	Psoas Muscle	Psoas
43	chr20:25063800-25064400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
44	chr20:25063800-25064600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
45	chr20:25063800-25064600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr20:25063800-25064600	Bivalent Enhancer	Fetal Thymus	thymus
47	chr20:25063800-25064800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr20:25063800-25064800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr20:25063800-25065200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
50	chr20:25063800-25065200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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