Variant report

Variant	rs655580
Chromosome Location	chr19:53039110-53039111
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	POLR2A	chr19:53039070-53039954	GM19099	blood:	n/a	n/a
2	CTCF	chr19:53039020-53039170	BJ	skin:	n/a	n/a
3	CTCF	chr19:53039092-53039223	Spleen_OC	spleen:	n/a	n/a
4	POLR2A	chr19:53038986-53039865	MCF-7	breast:	n/a	n/a
5	CHD2	chr19:53039022-53039971	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:53039073-53039857	Raji	blood:	n/a	n/a
7	E2F4	chr19:53038899-53039754	MCF10A-Er-Src	breast:	n/a	chr19:53039201-53039209 chr19:53039195-53039205 chr19:53039200-53039210 chr19:53039202-53039209 chr19:53039216-53039226 chr19:53039611-53039623 chr19:53039201-53039209
8	CTCF	chr19:53039060-53039210	GM12871	blood:	n/a	n/a
9	PML	chr19:53038976-53039949	GM12878	blood:	n/a	n/a
10	YY1	chr19:53038803-53039246	H1-hESC	embryonic stem cell:	n/a	chr19:53039124-53039135
11	CTCF	chr19:53039080-53039230	HBMEC	blood vessel:	n/a	n/a
12	JUND	chr19:53038617-53039410	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:53038420-53040018	H1-hESC	embryonic stem cell:	n/a	n/a
14	NRF1	chr19:53039097-53039501	GM12878	blood:	n/a	n/a
15	ELF1	chr19:53039035-53039725	SK-N-SH	brain:	n/a	chr19:53039125-53039137
16	POLR2A	chr19:53038904-53039918	GM12878	blood:	n/a	n/a
17	CTCF	chr19:53039040-53039190	HPAF	blood vessel:	n/a	n/a
18	CTCF	chr19:53039060-53039210	AG10803	skin:	n/a	n/a
19	CTCF	chr19:53039040-53039190	BJ	skin:	n/a	n/a
20	ZEB1	chr19:53039061-53039276	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:53039089-53039978	MCF-7	breast:	n/a	n/a
22	CTCF	chr19:53039020-53039170	HMF	breast:	n/a	n/a
23	CTCF	chr19:53039060-53039210	GM12870	blood:	n/a	n/a
24	MAX	chr19:53039057-53039523	MCF-7	breast:	n/a	chr19:53039131-53039141
25	POLR2A	chr19:53039099-53039794	GM12891	blood:	n/a	n/a
26	CTCF	chr19:53039020-53039170	HFF	foreskin:	n/a	n/a
27	POLR2A	chr19:53038928-53039937	GM12892	blood:	n/a	n/a
28	POLR2A	chr19:53038521-53040036	GM12892	blood:	n/a	n/a
29	CTCF	chr19:53039040-53039190	HVMF	connective:	n/a	n/a
30	CTCF	chr19:53039060-53039210	HFF-Myc	foreskin:	n/a	n/a
31	MXI1	chr19:53038906-53039416	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr19:53039020-53039170	AG04450	lung:	n/a	n/a
33	POLR2A	chr19:53038626-53040058	GM12892	blood:	n/a	n/a
34	MXI1	chr19:53038928-53039908	GM12878	blood:	n/a	n/a
35	CTCF	chr19:53039040-53039190	HCM	heart:	n/a	n/a
36	POLR2A	chr19:53039070-53039854	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:53039072-53039853	Gliobla	brain:	n/a	n/a
38	CTCF	chr19:53039040-53039190	HRE	kidney:	n/a	n/a
39	CTCF	chr19:53039080-53039230	HPF	lung:	n/a	n/a
40	POLR2A	chr19:53038958-53039649	HUVEC	blood vessel:	n/a	n/a
41	CTCF	chr19:53039040-53039190	GM12872	blood:	n/a	n/a
42	POLR2A	chr19:53039051-53039487	MCF10A-Er-Src	breast:	n/a	n/a
43	NFATC1	chr19:53039070-53039563	GM12878	blood:	n/a	n/a
44	CTCF	chr19:53039060-53039210	HPAF	blood vessel:	n/a	n/a
45	POLR2A	chr19:53039050-53039938	GM15510	blood:	n/a	n/a
46	CTCF	chr19:53039040-53039190	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr19:53039040-53039190	HBMEC	blood vessel:	n/a	n/a
48	TAF1	chr19:53038571-53039616	H1-hESC	embryonic stem cell:	n/a	n/a
49	MXI1	chr19:53038730-53039938	IMR90	lung:	n/a	n/a
50	POLR2A	chr19:53039010-53039996	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53029459..53032258-chr19:53036873..53039549,6	MCF-7	breast:

Variant related genes	Relation type
ZNF808	TF binding region
ENSG00000198482	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2608522	0.81[ASN][1000 genomes]
rs376595	0.81[ASN][1000 genomes]
rs396663	0.81[ASN][1000 genomes]
rs400709	0.81[ASN][1000 genomes]
rs417599	0.81[ASN][1000 genomes]
rs422195	0.81[ASN][1000 genomes]
rs434709	0.81[ASN][1000 genomes]
rs439618	0.81[ASN][1000 genomes]
rs445500	0.80[ASN][1000 genomes]
rs4802971	0.81[ASN][1000 genomes]
rs4802972	0.81[ASN][1000 genomes]
rs62117197	0.81[ASN][1000 genomes]
rs62117198	0.81[ASN][1000 genomes]
rs62117199	0.83[ASN][1000 genomes]
rs688646	0.80[ASN][1000 genomes]
rs781129	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53032200-53039400	Weak transcription	Stomach Mucosa	stomach
2	chr19:53032200-53057000	Weak transcription	Hela-S3	cervix
3	chr19:53032600-53039200	Weak transcription	Spleen	Spleen
4	chr19:53032600-53049800	Weak transcription	HepG2	liver
5	chr19:53033800-53040200	ZNF genes & repeats	Liver	Liver
6	chr19:53036400-53040000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:53036400-53040400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
8	chr19:53037000-53039200	Enhancers	Fetal Heart	heart
9	chr19:53037400-53040400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
10	chr19:53037600-53051800	Weak transcription	K562	blood
11	chr19:53038000-53039200	Flanking Active TSS	Dnd41	blood
12	chr19:53038000-53040800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr19:53038200-53039400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:53038200-53039800	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:53038200-53040000	Active TSS	Fetal Brain Female	brain
16	chr19:53038200-53040200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr19:53038200-53040200	Active TSS	GM12878-XiMat	blood
18	chr19:53038200-53040400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:53038400-53039200	Active TSS	Brain Germinal Matrix	brain
20	chr19:53038400-53039600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:53038400-53039600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:53038400-53039600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:53038400-53040000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr19:53038400-53040000	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr19:53038400-53040000	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr19:53038400-53040200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr19:53038400-53040200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:53038400-53040400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr19:53038400-53040400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:53038400-53040400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:53038400-53040400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:53038600-53039200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr19:53038600-53039200	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr19:53038600-53039200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr19:53038600-53039200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:53038600-53039200	Flanking Active TSS	Placenta	Placenta
37	chr19:53038600-53039400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:53038600-53039400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:53038600-53039400	Active TSS	Brain Anterior Caudate	brain
40	chr19:53038600-53039400	Active TSS	Rectal Smooth Muscle	rectum
41	chr19:53038600-53039800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:53038600-53039800	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr19:53038600-53039800	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr19:53038600-53039800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:53038600-53039800	Active TSS	Aorta	Aorta
46	chr19:53038600-53039800	Active TSS	Fetal Intestine Small	intestine
47	chr19:53038600-53039800	Active TSS	Fetal Thymus	thymus
48	chr19:53038600-53039800	Active TSS	Psoas Muscle	Psoas
49	chr19:53038600-53039800	Active TSS	Thymus	Thymus
50	chr19:53038600-53040000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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