Variant report

Variant	rs7344824
Chromosome Location	chr20:25062001-25062002
allele	A/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	REST	chr20:25061975-25062110	K562	blood:	n/a	n/a
3	CTCF	chr20:25061940-25062090	BE2_C	brain:	n/a	chr20:25062061-25062074
4	REST	chr20:25061642-25062164	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
5	REST	chr20:25061484-25062220	H1-hESC	embryonic stem cell:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
6	RAD21	chr20:25061803-25062286	H1-hESC	embryonic stem cell:	n/a	chr20:25061978-25061992
7	REST	chr20:25061158-25062456	ECC-1	luminal epithelium:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
8	CTCF	chr20:25061931-25062170	A549	lung:	n/a	chr20:25062061-25062074
9	REST	chr20:25061399-25062180	A549	lung:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
10	REST	chr20:25061565-25062273	H1-neurons	neurons:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
11	CTCF	chr20:25061983-25062113	A549	lung:	n/a	chr20:25062061-25062074
12	CHD2	chr20:25061649-25062293	H1-hESC	embryonic stem cell:	n/a	n/a
13	SUZ12	chr20:25061549-25065864	NT2-D1	testis:	n/a	n/a
14	REST	chr20:25061317-25062186	PFSK-1	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
15	CTCF	chr20:25061969-25062254	A549	lung:	n/a	chr20:25062061-25062074
16	CTBP2	chr20:25061593-25062487	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIN3AK20	chr20:25061613-25062034	H1-hESC	embryonic stem cell:	n/a	n/a
18	REST	chr20:25061458-25062106	HCT-116	colon:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
19	CTCF	chr20:25061980-25062130	HBMEC	blood vessel:	n/a	chr20:25062061-25062074
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	chr20:25061492-25062187	SK-N-SH	brain:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
23	RAD21	chr20:25061844-25062280	A549	lung:	n/a	chr20:25061978-25061992
24	REST	chr20:25061294-25062307	PANC-1	pancreas:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
25	CTCF	chr20:25061925-25062235	H1-hESC	embryonic stem cell:	n/a	chr20:25062061-25062074
26	REST	chr20:25061128-25062227	ECC-1	luminal epithelium:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
27	REST	chr20:25061608-25062518	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
28	REST	chr20:25061395-25062174	MCF-7	breast:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
29	REST	chr20:25061557-25062002	K562	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
30	CTCF	chr20:25061960-25062110	HRE	kidney:	n/a	chr20:25062061-25062074
31	RAD21	chr20:25061847-25062240	HepG2	liver:	n/a	chr20:25061978-25061992
32	POLR2A	chr20:25061951-25062222	H1-neurons	neurons:	n/a	n/a
33	CTCF	chr20:25061980-25062130	GM12864	blood:	n/a	chr20:25062061-25062074
34	CTCF	chr20:25061860-25062010	SK-N-SH_RA	brain:	n/a	n/a
35	MAX	chr20:25061676-25062234	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr20:25061885-25062101	A549	lung:	n/a	chr20:25062061-25062074
37	REST	chr20:25061538-25062013	HCT-116	colon:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
38	RAD21	chr20:25061723-25062340	H1-hESC	embryonic stem cell:	n/a	chr20:25061978-25061992
39	RAD21	chr20:25061997-25062079	HepG2	liver:	n/a	n/a
40	REST	chr20:25061376-25062443	H1-hESC	embryonic stem cell:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
41	RCOR1	chr20:25061631-25062513	HepG2	liver:	n/a	n/a
42	REST	chr20:25061267-25062399	A549	lung:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
43	RAD21	chr20:25061587-25062407	H1-hESC	embryonic stem cell:	n/a	chr20:25061978-25061992
44	CTCF	chr20:25061943-25062184	Medullo	brain:	n/a	chr20:25062061-25062074
45	REST	chr20:25061397-25062115	MCF-7	breast:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
46	REST	chr20:25061353-25062229	HepG2	liver:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968
47	CTCF	chr20:25061956-25062193	H1-hESC	embryonic stem cell:	n/a	chr20:25062061-25062074
48	CTCF	chr20:25061940-25062090	GM12871	blood:	n/a	chr20:25062061-25062074
49	MAX	chr20:25061696-25062161	H1-hESC	embryonic stem cell:	n/a	n/a
50	REST	chr20:25061483-25062126	GM12878	blood:	n/a	chr20:25061740-25061758 chr20:25061820-25061829 chr20:25061955-25061968

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

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]
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	0.90[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]
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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25060600-25062600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr20:25061600-25062400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr20:25061600-25064600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
4	chr20:25061800-25062200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr20:25061800-25062200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:25061800-25062200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:25061800-25062200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr20:25061800-25062200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
9	chr20:25061800-25062200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
10	chr20:25061800-25062200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
11	chr20:25061800-25062200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr20:25061800-25062200	Bivalent Enhancer	Fetal Lung	lung
13	chr20:25061800-25062200	Bivalent Enhancer	Fetal Stomach	stomach
14	chr20:25061800-25062200	Bivalent Enhancer	Fetal Thymus	thymus
15	chr20:25061800-25062200	Bivalent Enhancer	Left Ventricle	heart
16	chr20:25061800-25062200	Flanking Bivalent TSS/Enh	Right Ventricle	heart
17	chr20:25061800-25062400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr20:25061800-25062400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:25061800-25062400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:25061800-25062400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr20:25061800-25062400	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr20:25061800-25062600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr20:25061800-25062600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr20:25061800-25062600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
25	chr20:25061800-25062600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
26	chr20:25061800-25062600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr20:25061800-25062600	Bivalent Enhancer	Lung	lung
28	chr20:25061800-25062600	Bivalent Enhancer	Ovary	ovary
29	chr20:25061800-25062600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
30	chr20:25061800-25062800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:25061800-25062800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr20:25061800-25062800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr20:25061800-25062800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr20:25061800-25062800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr20:25061800-25062800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr20:25061800-25062800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr20:25061800-25062800	Enhancers	Gastric	stomach
38	chr20:25061800-25062800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
39	chr20:25061800-25062800	Flanking Bivalent TSS/Enh	Thymus	Thymus
40	chr20:25061800-25063000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
41	chr20:25061800-25063000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr20:25061800-25063000	Bivalent Enhancer	Spleen	Spleen
43	chr20:25061800-25063400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr20:25061800-25063800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
45	chr20:25061800-25064000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr20:25061800-25064000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
47	chr20:25061800-25065800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr20:25061800-25065800	Bivalent Enhancer	Fetal Brain Male	brain
49	chr20:25061800-25065800	Enhancers	Pancreas	Pancrea
50	chr20:25062000-25062200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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