Variant report

Variant	rs6050304
Chromosome Location	chr20:25061798-25061799
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	REST	chr20:25061637-25062011	PANC-1	pancreas:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
2	JUND	chr20:25061742-25061864	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr20:25061642-25062164	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
4	REST	chr20:25061484-25062220	H1-hESC	embryonic stem cell:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
5	REST	chr20:25061669-25061956	GM12878	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829
6	REST	chr20:25061158-25062456	ECC-1	luminal epithelium:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
7	REST	chr20:25061399-25062180	A549	lung:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
8	ZNF143	chr20:25061713-25061883	K562	blood:	n/a	chr20:25061763-25061773
9	REST	chr20:25061565-25062273	H1-neurons	neurons:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
10	CHD2	chr20:25061649-25062293	H1-hESC	embryonic stem cell:	n/a	n/a
11	SUZ12	chr20:25061549-25065864	NT2-D1	testis:	n/a	n/a
12	REST	chr20:25061317-25062186	PFSK-1	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
13	CTBP2	chr20:25061593-25062487	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3AK20	chr20:25061613-25062034	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr20:25061458-25062106	HCT-116	colon:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
16	REST	chr20:25061646-25061969	U87	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
17	RCOR1	chr20:25061793-25061892	K562	blood:	n/a	n/a
18	PBX3	chr20:25061790-25061970	GM12878	blood:	n/a	n/a
19	CTCF	chr20:25061680-25061830	A549	lung:	n/a	n/a
20	ZNF143	chr20:25061608-25062513	H1-hESC	embryonic stem cell:	n/a	chr20:25061763-25061773 chr20:25062207-25062225
21	REST	chr20:25061341-25062199	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
22	REST	chr20:25061527-25061998	U87	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
23	REST	chr20:25061492-25062187	SK-N-SH	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
24	REST	chr20:25061294-25062307	PANC-1	pancreas:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
25	SIN3AK20	chr20:25061643-25061969	H1-hESC	embryonic stem cell:	n/a	n/a
26	REST	chr20:25061128-25062227	ECC-1	luminal epithelium:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
27	REST	chr20:25061595-25061992	GM12878	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
28	REST	chr20:25061608-25062518	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
29	REST	chr20:25061395-25062174	MCF-7	breast:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
30	REST	chr20:25061557-25062002	K562	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
31	REST	chr20:25061642-25061969	SK-N-SH	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
32	MAX	chr20:25061676-25062234	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr20:25061538-25062013	HCT-116	colon:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
34	REST	chr20:25061697-25061921	PFSK-1	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829
35	RAD21	chr20:25061723-25062340	H1-hESC	embryonic stem cell:	n/a	chr20:25061978-25061992
36	REST	chr20:25061376-25062443	H1-hESC	embryonic stem cell:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
37	RCOR1	chr20:25061631-25062513	HepG2	liver:	n/a	n/a
38	REST	chr20:25061267-25062399	A549	lung:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
39	RAD21	chr20:25061587-25062407	H1-hESC	embryonic stem cell:	n/a	chr20:25061978-25061992
40	REST	chr20:25061584-25061961	SK-N-SH	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829
41	REST	chr20:25061397-25062115	MCF-7	breast:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
42	REST	chr20:25061353-25062229	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
43	GABPA	chr20:25061746-25061888	HepG2	liver:	n/a	n/a
44	REST	chr20:25061569-25061996	PANC-1	pancreas:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
45	MAX	chr20:25061696-25062161	H1-hESC	embryonic stem cell:	n/a	n/a
46	REST	chr20:25061483-25062126	GM12878	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
47	GABPA	chr20:25061649-25061956	H1-hESC	embryonic stem cell:	n/a	n/a
48	REST	chr20:25061577-25061976	Hela-S3	cervix:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
49	REST	chr20:25061290-25062145	PANC-1	pancreas:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
50	REST	chr20:25061411-25062291	HL-60	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:25061762-25061812	GM19239	blood:	n/a
2	chr20:25061762-25061812	ECC-1	luminal epithelium:	n/a
3	chr20:25061762-25061812	Hela-S3	cervix:	n/a
4	chr20:25061762-25061812	AG09309	skin:	n/a
5	chr20:25061762-25061812	HUVEC	blood vessel:	n/a
6	chr20:25061762-25061812	HL-60	blood:	n/a
7	chr20:25061762-25061812	GM12878	blood:	n/a
8	chr20:25061762-25061812	SAEC	small airway:	n/a
9	chr20:25061762-25061812	Caco-2	colon:	n/a
10	chr20:25061762-25061812	HEK293	kidney:	embryo
11	chr20:25061762-25061812	HNPCEpiC	eye:	n/a
12	chr20:25061762-25061812	K562	blood:	n/a
13	chr20:25061762-25061812	HAEpiC	amniotic membrane:	n/a
14	chr20:25061762-25061812	Jurkat	blood:	n/a
15	chr20:25061762-25061812	BJ	skin:	n/a
16	chr20:25061762-25061812	HIPEpiC	eye:	n/a
17	chr20:25061762-25061812	AG04449	skin:	fetal
18	chr20:25061762-25061812	PFSK-1	brain:	n/a
19	chr20:25061762-25061812	NH-A	brain:	n/a
20	chr20:25061762-25061812	ovcar-3	ovarian:	n/a
21	chr20:25061762-25061812	MCF-7	breast:	n/a
22	chr20:25061762-25061812	AG10803	skin:	n/a
23	chr20:25061762-25061812	HRE	kidney:	n/a
24	chr20:25061762-25061812	ProgFib	skin:	n/a
25	chr20:25061762-25061812	HEEpiC	esophagus:	n/a
26	chr20:25061762-25061812	GM12892	blood:	n/a
27	chr20:25061762-25061812	A549	lung:	n/a
28	chr20:25061762-25061812	HCF	heart:	n/a
29	chr20:25061762-25061812	NHBE	bronchial:	n/a
30	chr20:25061762-25061812	HCT-116	colon:	n/a
31	chr20:25061762-25061812	SK-N-SH_RA	brain:	n/a
32	chr20:25061762-25061812	AoSMC	blood vessel:	n/a
33	chr20:25061762-25061812	AG09319	gingival:	n/a
34	chr20:25061762-25061812	LNCaP	prostate:	n/a
35	chr20:25061762-25061812	NHDF-neo	bronchial:	n/a
36	chr20:25061762-25061812	RPTEC	kidney:	n/a
37	chr20:25061762-25061812	Hepatocyte	liver:	n/a
38	chr20:25061762-25061812	HRCEpiC	kidney:	n/a
39	chr20:25061762-25061812	NT2-D1	testis:	n/a
40	chr20:25061762-25061812	PrEC	prostate:	n/a
41	chr20:25061762-25061812	SKMC	muscle:	n/a
42	chr20:25061762-25061812	NB4	blood:	n/a
43	chr20:25061762-25061812	CMK	blood:	n/a
44	chr20:25061762-25061812	GM06990	blood:	n/a
45	chr20:25061762-25061812	AG04450	lung:	fetal
46	chr20:25061762-25061812	HPAEpiC	pulmonary alveolar:	n/a
47	chr20:25061762-25061812	IMR90	lung:	fetal
48	chr20:25061762-25061812	U87	brain:	n/a
49	chr20:25061762-25061812	SK-N-SH	brain:	n/a
50	chr20:25061762-25061812	HepG2	liver:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25054332..25057280-chr20:25059401..25062693,3	K562	blood:

Variant related genes	Relation type
VSX1	TF binding region
VSX1	CpG island

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

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

rs_ID	r²[population]
rs1005409	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	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[ASN][1000 genomes]
rs2387577	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4813546	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	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	0.96[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]
rs6037014	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	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]
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	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	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]
rs6083739	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[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	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	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:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25058800-25061800	Weak transcription	Pancreas	Pancrea
2	chr20:25060600-25062600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr20:25061600-25061800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:25061600-25062000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
5	chr20:25061600-25062400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr20:25061600-25064600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood

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